Annotations: 9V0C

Cryo-EM structure of iberdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth U]	Ubiquitin	RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome protein tag activity molecular tag activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytoplasm cytosol cell periphery plasma membrane nucleoplasm organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle cytosolic ribosome ribosome protein-containing complex preribosome nuclear protein-containing complex small-subunit processome ribonucleoprotein complex synapse cell junction endosome membrane endosome mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane
G [auth R]	E3 ubiquitin-protein ligase RBX1, N-terminally processed	protein-containing complex binding binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cullin family protein binding aminoacyltransferase activity ubiquitin-like protein transferase activity NEDD8 transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity protein-containing complex binding binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding cullin family protein binding aminoacyltransferase activity ubiquitin-like protein transferase activity NEDD8 transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity NEDD8 ligase activity ubiquitin-like protein ligase activity ubiquitin-protein transferase activity ubiquitin-ubiquitin ligase activity ubiquitin protein ligase activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion biological regulation regulation of mitophagy regulation of catabolic process negative regulation of mitophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy cellular process metabolic process regulation of metabolic process autophagy of mitochondrion microtubule organizing center organization microtubule cytoskeleton organization cellular component organization centrosome duplication organelle organization centrosome cycle microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization cell cycle process positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of protein catabolic process ribosome-associated ubiquitin-dependent protein catabolic process cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction cell communication cellular response to endogenous stimulus signal transduction BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of signaling regulation of BMP signaling pathway cell surface receptor signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus response to BMP regulation of response to stimulus regulation of cell communication response to growth factor transforming growth factor beta receptor superfamily signaling pathway macromolecule modification post-translational protein modification protein modification process developmental process multicellular organism development multicellular organismal process limb development appendage development anatomical structure development animal gross anatomical part developmental process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription ubiquitin-dependent protein catabolic process via the C-end degron rule pathway protein polyubiquitination protein ubiquitination protein K48-linked ubiquitination protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of miRNA-mediated gene silencing post-transcriptional regulation of gene expression regulation of gene silencing by regulatory ncRNA regulation of post-transcriptional gene silencing by regulatory ncRNA negative regulation of macromolecule metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing negative regulation of gene expression regulation of post-transcriptional gene silencing negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing DNA metabolic process nucleotide-excision repair DNA damage response DNA repair negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive regulation of signaling rhythmic process circadian rhythm regulation of circadian rhythm protein neddylation regulation of cellular response to stress regulation of response to stress regulation of protein modification process regulation of protein autoubiquitination regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification protein autoubiquitination positive regulation of protein autoubiquitination regulation of DNA-templated DNA replication initiation DNA-templated DNA replication DNA replication initiation DNA replication regulation of DNA-templated DNA replication regulation of DNA replication regulation of DNA metabolic process fat cell differentiation regulation of developmental process cellular developmental process negative regulation of developmental process regulation of cell differentiation negative regulation of fat cell differentiation negative regulation of beige fat cell differentiation cell differentiation beige fat cell differentiation negative regulation of cell differentiation regulation of fat cell differentiation cell population proliferation regulation of cell population proliferation regulation of embryonic development regulation of multicellular organismal development embryo development regulation of multicellular organismal process TOR signaling regulation of TOR signaling intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of stem cell population maintenance maintenance of cell number stem cell population maintenance negative regulation of type I interferon production cytokine production regulation of cytokine production type I interferon production negative regulation of cytokine production negative regulation of multicellular organismal process regulation of type I interferon production spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation DNA-templated DNA replication maintenance of fidelity replication fork processing neural crest cell differentiation animal organ development mesenchyme development tissue development stem cell differentiation mesenchymal cell differentiation protein K27-linked ubiquitination epigenetic regulation of gene expression chromatin organization chromatin remodeling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of cell communication negative regulation of Wnt signaling pathway Wnt signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of cellular component organization regulation of centrosome cycle regulation of cell cycle process regulation of microtubule-based process regulation of centrosome duplication regulation of cell cycle regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death transcription-coupled nucleotide-excision repair DNA damage checkpoint signaling regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition regulation of cell cycle checkpoint negative regulation of cell cycle phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage regulation of DNA damage checkpoint regulation of response to oxidative stress negative regulation of response to oxidative stress MAPK cascade cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway regulation of cellular response to insulin stimulus cell surface receptor protein tyrosine kinase signaling pathway response to hormone cellular response to hormone stimulus regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound negative regulation of cellular response to insulin stimulus negative regulation of insulin receptor signaling pathway response to insulin cellular response to insulin stimulus negative regulation of adipose tissue development connective tissue development adipose tissue development regulation of adipose tissue development cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid mitotic cell cycle process G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition protein monoubiquitination regulation of mitotic cell cycle RNA surveillance RNA catabolic process transcription initiation at RNA polymerase II promoter RNA polymerase II transcription initiation surveillance nuclear RNA surveillance DNA-templated transcription initiation nucleobase-containing compound catabolic process nucleic acid catabolic process negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus xenophagy response to biotic stimulus response to external biotic stimulus regulation of xenophagy response to other organism defense response response to external stimulus defense response to other organism SCF-dependent proteasomal ubiquitin-dependent protein catabolic process organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly cilium organization cell projection assembly positive regulation of TORC1 signaling positive regulation of TOR signaling regulation of TORC1 signaling TORC1 signaling T cell activation immune system process cell activation lymphocyte activation leukocyte activation regulation of defense response regulation of inflammatory response inflammatory response response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV negative regulation of DNA-templated DNA replication negative regulation of DNA replication negative regulation of DNA metabolic process regulation of cytokinesis cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis regulation of cell division regulation of mitotic cytokinesis cell division regulation of leukocyte activation regulation of cell activation natural killer cell activation regulation of immune system process regulation of natural killer cell activation regulation of lymphocyte activation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytoplasmic ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex VCB complex cullin-RING ubiquitin ligase complex Cul5-RING ubiquitin ligase complex Cul4-RING E3 ubiquitin ligase complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytoplasmic ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex VCB complex cullin-RING ubiquitin ligase complex Cul5-RING ubiquitin ligase complex Cul4-RING E3 ubiquitin ligase complex Cul4A-RING E3 ubiquitin ligase complex intracellular organelle organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome membrane-bounded organelle Golgi apparatus intracellular membrane-bounded organelle endomembrane system centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen SCF ubiquitin ligase complex Cul7-RING ubiquitin ligase complex Cul3-RING ubiquitin ligase complex Cul4B-RING E3 ubiquitin ligase complex Cul2-RING ubiquitin ligase complex
F [auth N]	NEDD8	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to nitrogen compound response to stimulus catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to nitrogen compound response to stimulus response to alcohol response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound response to alkaloid cellular response to chemical stimulus cellular response to alcohol response to camptothecin cellular response to camptothecin response to chemical cellular response to alkaloid macromolecule modification protein modification process multicellular organismal process regulation of cellular component organization regulation of cellular process cellular component organization cellular component biogenesis multicellular organism development cellular component assembly regulation of postsynapse assembly cell junction assembly anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development developmental process regulation of biological process postsynapse organization postsynapse assembly biological regulation regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly animal gross anatomical part developmental process regulation of protein metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis regulation of metabolic process post-translational protein modification protein neddylation protein modification by small protein conjugation protein modification by small protein conjugation or removal anatomical structure morphogenesis	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol postsynapse synapse extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol postsynapse synapse cell junction nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen glutamatergic synapse
E [auth I]	Zinc finger protein Aiolos	histone deacetylase binding protein binding binding enzyme binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding histone deacetylase binding protein binding binding enzyme binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein dimerization activity transcription regulator activity DNA-binding transcription factor activity chromatin binding promoter-specific chromatin binding identical protein binding protein homodimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process leukocyte differentiation tissue development animal gross anatomical part developmental process mesoderm development regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation apoptotic process regulation of programmed cell death cell death programmed cell death RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process T cell activation T cell differentiation regulation of leukocyte differentiation regulation of developmental process regulation of leukocyte activation regulation of cell activation regulation of cell differentiation regulation of cell development regulation of B cell differentiation multicellular organism development regulation of B cell activation regulation of immune system process regulation of multicellular organismal process regulation of lymphocyte differentiation regulation of multicellular organismal development regulation of hemopoiesis regulation of lymphocyte activation leukocyte proliferation regulation of B cell proliferation lymphocyte proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation B cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of mononuclear cell proliferation regulation of primary metabolic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
D	Ubiquitin-conjugating enzyme E2 D1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination protein ubiquitination macromolecule modification catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein K48-linked ubiquitination cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication negative regulation of TORC1 signaling regulation of intracellular signal transduction negative regulation of TOR signaling negative regulation of cellular process signal transduction regulation of TORC1 signaling TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling negative regulation of response to stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus regulation of cell communication TORC1 signaling regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process regulation of metabolic process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway cellular response to endogenous stimulus BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus cell surface receptor signaling pathway regulation of BMP signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex
C [auth B]	DNA damage-binding protein 1	protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding nucleic acid binding protein-containing complex binding protein binding cullin family protein binding damaged DNA binding WD40-repeat domain binding protein domain specific binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process regulation of biological process regulation of developmental process biological regulation regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process regulation of biological process regulation of developmental process biological regulation regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number stem cell population maintenance spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process macromolecule metabolic process replication fork processing catabolic process proteasomal protein catabolic process protein catabolic process protein metabolic process macromolecule catabolic process cell population proliferation regulation of biosynthetic process regulation of cellular process epigenetic regulation of gene expression regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process cellular component organization or biogenesis regulation of metabolic process regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process negative regulation of adipose tissue development connective tissue development adipose tissue development negative regulation of developmental process animal organ development negative regulation of biological process tissue development regulation of adipose tissue development anatomical structure development negative regulation of multicellular organismal process animal gross anatomical part developmental process epigenetic programming of gene expression epigenetic programming in the zygotic pronuclei regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle mitotic cell cycle phase transition cell cycle process DNA repair positive regulation of viral genome replication positive regulation of viral process positive regulation of biological process viral life cycle regulation of viral life cycle regulation of viral process viral genome replication viral process regulation of viral genome replication regulation of miRNA-mediated gene silencing post-transcriptional regulation of gene expression regulation of gene silencing by regulatory ncRNA negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA negative regulation of macromolecule metabolic process negative regulation of metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing negative regulation of gene expression regulation of post-transcriptional gene silencing negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing nucleotide-excision repair response to light stimulus cellular response to environmental stimulus cellular response to light stimulus cellular response to radiation response to UV UV-damage excision repair response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV monosaccharide metabolic process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process regulation of gluconeogenesis positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process glucose metabolic process rhythmic process circadian rhythm regulation of circadian rhythm positive regulation of protein metabolic process positive regulation of macromolecule metabolic process regulation of protein metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process regulation of cellular response to stress regulation of response to stimulus regulation of response to stress biological process involved in interspecies interaction between organisms biological process involved in interaction with symbiont biological process involved in symbiotic interaction regulation by virus of viral protein levels in host cell positive regulation by virus of viral protein levels in host cell regulation of biological quality proteasome-mediated ubiquitin-dependent protein catabolic process regulation of DNA-templated DNA replication initiation DNA replication initiation regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of DNA replication regulation of DNA metabolic process exit from host cell viral release from host cell biological process involved in interaction with host regulation of cell population proliferation meiotic chromosome segregation microtubule cytoskeleton organization membraneless organelle assembly female gamete generation meiotic cell cycle process cellular component biogenesis cellular component assembly female meiotic nuclear division meiotic nuclear division chromosome segregation spindle organization organelle assembly organelle fission meiotic cell cycle meiotic spindle organization meiotic spindle assembly spindle assembly nuclear division organelle organization nuclear chromosome segregation microtubule-based process cytoskeleton organization spindle assembly involved in female meiosis regulation of embryonic development regulation of multicellular organismal development embryo development multicellular organism development autophagy regulation of autophagy process utilizing autophagic mechanism regulation of cytokinesis cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis regulation of cell division regulation of mitotic cytokinesis cell division regulation of leukocyte activation cell activation regulation of cell activation natural killer cell activation lymphocyte activation leukocyte activation immune system process regulation of immune system process regulation of natural killer cell activation regulation of lymphocyte activation	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle membraneless organelle intracellular membraneless organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm intracellular organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex nucleoplasm site of double-strand break site of DNA damage Cul4B-RING E3 ubiquitin ligase complex
B [auth A]	Cullin-4A	protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin protein ligase binding protein binding protein complex scaffold activity ubiquitin ligase complex scaffold activity structural molecule activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process regulation of biological process regulation of developmental process biological regulation regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process regulation of biological process regulation of developmental process biological regulation regulation of stem cell population maintenance regulation of multicellular organismal process maintenance of cell number stem cell population maintenance spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process macromolecule metabolic process replication fork processing regulation of cellular process signaling cell death intracellular signal transduction cell communication apoptotic signaling pathway signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition cell cycle regulation of cell cycle cell cycle process cell population proliferation regulation of biosynthetic process epigenetic regulation of gene expression regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process regulation of metabolic process regulation of apoptotic process regulation of programmed cell death catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of cellular response to stress regulation of response to stimulus regulation of response to stress proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of DNA-templated DNA replication initiation DNA replication initiation regulation of DNA-templated DNA replication regulation of nucleobase-containing compound metabolic process regulation of DNA replication regulation of DNA metabolic process multicellular organism development embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development animal gross anatomical part developmental process T cell activation immune system process cell activation lymphocyte activation leukocyte activation negative regulation of adipose tissue development connective tissue development adipose tissue development negative regulation of developmental process animal organ development negative regulation of biological process tissue development regulation of adipose tissue development negative regulation of multicellular organismal process ubiquitin-dependent protein catabolic process via the C-end degron rule pathway rhythmic process response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV mitotic cell cycle process G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition regulation of miRNA-mediated gene silencing post-transcriptional regulation of gene expression regulation of gene silencing by regulatory ncRNA negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA negative regulation of macromolecule metabolic process negative regulation of metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing negative regulation of gene expression regulation of post-transcriptional gene silencing negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of cell population proliferation nucleotide-excision repair DNA repair regulation of embryonic development regulation of multicellular organismal development autophagy regulation of autophagy process utilizing autophagic mechanism regulation of cytokinesis cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis regulation of cell division regulation of mitotic cytokinesis cell division regulation of leukocyte activation regulation of cell activation natural killer cell activation regulation of immune system process regulation of natural killer cell activation regulation of lymphocyte activation	cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
A [auth C]	Protein cereblon	protein binding binding transmembrane transporter binding cation binding ion binding metal ion binding small molecule binding	regulation of localization regulation of biological process regulation of cellular process transport regulation of transport negative regulation of monoatomic ion transport regulation of monoatomic ion transport monoatomic ion transmembrane transport biological regulation negative regulation of biological process negative regulation of transport regulation of monoatomic ion transmembrane transport establishment of localization negative regulation of transmembrane transport transmembrane transport regulation of localization regulation of biological process regulation of cellular process transport regulation of transport negative regulation of monoatomic ion transport regulation of monoatomic ion transport monoatomic ion transmembrane transport biological regulation negative regulation of biological process negative regulation of transport regulation of monoatomic ion transmembrane transport establishment of localization negative regulation of transmembrane transport transmembrane transport localization regulation of transmembrane transport negative regulation of monoatomic ion transmembrane transport negative regulation of cellular process monoatomic ion transport cellular process developmental process multicellular organism development multicellular organismal process limb development appendage development anatomical structure development animal gross anatomical part developmental process cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component organization cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal negative regulation of cellular component organization negative regulation of protein-containing complex assembly catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process behavior locomotory behavior exploration behavior locomotory exploration behavior	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex Cul4A-RING E3 ubiquitin ligase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H [auth U]	IPR019954	Ubiquitin conserved site	Conserved Site
H [auth U]	IPR038582	Small ribosomal subunit protein eS31 eukaryotic superfamily	Homologous Superfamily
H [auth U]	IPR050158	Ubiquitin and ubiquitin-like	Family
H [auth U]	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily
H [auth U]	IPR000626	Ubiquitin-like domain	Domain
H [auth U]	IPR002906	Small ribosomal subunit protein eS31	Domain
H [auth U]	IPR019956	Ubiquitin domain	Domain
H [auth U]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
G [auth R]	IPR024766	Zinc finger, RING-H2-type	Domain
G [auth R]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
G [auth R]	IPR051031	RING-box E3 Ubiquitin Ligase	Family
G [auth R]	IPR001841	Zinc finger, RING-type	Domain
F [auth N]	IPR019954	Ubiquitin conserved site	Conserved Site
F [auth N]	IPR000626	Ubiquitin-like domain	Domain
F [auth N]	IPR019956	Ubiquitin domain	Domain
F [auth N]	IPR050158	Ubiquitin and ubiquitin-like	Family
F [auth N]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
F [auth N]	IPR038738	Nedd8-like ubiquitin	Domain
E [auth I]	IPR013087	Zinc finger C2H2-type	Domain
E [auth I]	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
E [auth I]	IPR050589	Ikaros C2H2-type zinc-finger	Family
D	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
D	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
D	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
C [auth B]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
C [auth B]	IPR058543	RSE1/DDB1/CPSF1, second beta-propeller	Domain
C [auth B]	IPR004871	RSE1/DDB1/CPSF1, C-terminal	Domain
C [auth B]	IPR050358	RSE1/DDB1/CPSF1	Family
C [auth B]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C [auth B]	IPR018846	RSE1/DDB1/CPSF1, first beta-propeller	Domain
B [auth A]	IPR045093	Cullin	Family
B [auth A]	IPR016158	Cullin homology domain	Domain
B [auth A]	IPR016157	Cullin, conserved site	Conserved Site
B [auth A]	IPR059120	Cullin-like, alpha+beta domain	Domain
B [auth A]	IPR001373	Cullin, N-terminal	Domain
B [auth A]	IPR019559	Cullin, neddylation domain	Domain
B [auth A]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR036317	Cullin homology domain superfamily	Homologous Superfamily
B [auth A]	IPR016159	Cullin repeat-like-containing domain superfamily	Homologous Superfamily
A [auth C]	IPR015947	PUA-like superfamily	Homologous Superfamily
A [auth C]	IPR046336	Lon protease, N-terminal domain superfamily	Homologous Superfamily
A [auth C]	IPR004910	Yippee/Mis18/Cereblon	Domain
A [auth C]	IPR003111	Lon protease, N-terminal domain	Domain
A [auth C]	IPR034750	CULT domain	Domain

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9V0C | pdb_00009v0c

Cryo-EM structure of iberdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage