9Q33 | pdb_00009q33

Cereblon Ternary Complex with Blimp1 and compound 5

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SET domain	8088213	3000162	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21549	PR domain zinc finger protein 2, PR domain (PRDM2_PR)	PR domain zinc finger protein 2, PR domain	This domain is found in PR domain zinc protein 2 from humans (PRDM2) and similar proteins from animals. PRDM2 is a histone methyltransferase that functions as a DNA-binding transcription factor. It contains a PR (PRDI-BF1 and RIZ1 homology) domain, w ...	This domain is found in PR domain zinc protein 2 from humans (PRDM2) and similar proteins from animals. PRDM2 is a histone methyltransferase that functions as a DNA-binding transcription factor. It contains a PR (PRDI-BF1 and RIZ1 homology) domain, which is a distinct SET domain, that is responsible for its catalytic activity (this entry). This domain displays a typical SET fold consisting mainly of short beta-strands and intervening loops including a pseudo-knot at the C terminus [1].	Domain
B	PF02190	ATP-dependent protease La (LON) substrate-binding domain (LON_substr_bdg)	ATP-dependent protease La (LON) substrate-binding domain	-	Family
B	PF03226	Yippee zinc-binding/DNA-binding /Mis18, centromere assembly (Yippee-Mis18)	Yippee zinc-binding/DNA-binding /Mis18, centromere assembly	This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of ...	This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus [5]. This entry also includes the CULT domain proteins such as Cereblon [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PR domain zinc finger protein 1	DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding 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 DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding 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 chromatin binding promoter-specific chromatin binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity histone methyltransferase binding protein binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	sebum secreting cell proliferation cell population proliferation cellular process epithelial cell proliferation developmental process heart development multicellular organismal process animal organ development ventricular septum development circulatory system development multicellular organism development cardiac septum development cardiac chamber development anatomical structure development sebum secreting cell proliferation cell population proliferation cellular process epithelial cell proliferation developmental process heart development multicellular organismal process animal organ development ventricular septum development circulatory system development multicellular organism development cardiac septum development cardiac chamber development anatomical structure development cardiac ventricle development system development response to stimulus immune response immune system process adaptive immune response regulation of leukocyte differentiation regulation of cellular process cellular developmental process regulation of developmental process regulation of leukocyte activation cell development regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte activation lymphocyte differentiation regulation of cell development extrathymic T cell differentiation leukocyte activation regulation of T cell differentiation T cell activation cell differentiation T cell differentiation regulation of immune system process regulation of multicellular organismal process regulation of lymphocyte differentiation regulation of biological process regulation of multicellular organismal development hemopoiesis cell activation biological regulation regulation of T cell activation regulation of hemopoiesis regulation of extrathymic T cell differentiation leukocyte differentiation regulation of lymphocyte activation sexual reproduction reproductive process multicellular organismal reproductive process cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation germ cell development regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process methylation biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of natural killer cell differentiation regulation of natural killer cell activation natural killer cell differentiation natural killer cell activation anatomical structure morphogenesis morphogenesis of a branching structure sensory organ development retina development in camera-type eye visual system development neural retina development neurogenesis eye morphogenesis neuron differentiation animal organ morphogenesis sensory system development camera-type eye morphogenesis eye development nervous system development retinal bipolar neuron differentiation glutamatergic neuron differentiation generation of neurons retina morphogenesis in camera-type eye sensory organ morphogenesis camera-type eye development artery development aorta development vasculature development blood vessel development blood vessel morphogenesis tube development tube morphogenesis artery morphogenesis photoreceptor cell differentiation eye photoreceptor cell differentiation photoreceptor cell development eye photoreceptor cell development neuron development cell differentiation involved in embryonic placenta development placenta development chordate embryonic development embryo development in utero embryonic development trophoblast giant cell differentiation embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development multi-multicellular organism process maternal process involved in female pregnancy maternal placenta development female pregnancy multi-organism reproductive process heart valve development regulation of alpha-beta T cell activation regulation of alpha-beta T cell differentiation alpha-beta T cell differentiation alpha-beta T cell activation NK T cell differentiation regulation of NK T cell differentiation cell fate commitment epithelium development digestive system development intestinal epithelial cell differentiation intestinal epithelial cell development tissue development digestive tract development epithelial cell differentiation epithelial cell development columnar/cuboidal epithelial cell development columnar/cuboidal epithelial cell differentiation regulation of cell population proliferation RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription 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 primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biological process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process coronary vasculature development kidney development renal system development post-embryonic development	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 cytoplasm nucleoplasm
B	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 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
A	IPR046341	SET domain superfamily	Homologous Superfamily
A	IPR050331	Zinc finger PRDM4/PRDM1/PRDM14-like	Family
A	IPR013087	Zinc finger C2H2-type	Domain
A	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A	IPR044413	PRDM1, PR/SET domain	Domain
A	IPR001214	SET domain	Domain
A	IPR016608	PR domain zinc finger protein 1	Family
B	IPR015947	PUA-like superfamily	Homologous Superfamily
B	IPR046336	Lon protease, N-terminal domain superfamily	Homologous Superfamily
B	IPR004910	Yippee/Mis18/Cereblon	Domain
B	IPR003111	Lon protease, N-terminal domain	Domain
B	IPR034750	CULT domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O75626	ulcerative colitis rheumatoid arthritis Sjogren syndrome systemic lupus erythematosus pancreatic ductal adenocarcinoma primary biliary cholangitis Sicca Syndrome spina bifida acne cystic fibrosis gastric cancer inflammatory bowel disease lung carcinoma malignant pancreatic neoplasm osteosarcoma ulcerative colitis rheumatoid arthritis Sjogren syndrome systemic lupus erythematosus pancreatic ductal adenocarcinoma primary biliary cholangitis Sicca Syndrome spina bifida acne cystic fibrosis gastric cancer inflammatory bowel disease lung carcinoma malignant pancreatic neoplasm osteosarcoma pilocytic astrocytoma psoriasis acute myeloid leukemia diffuse large B-cell lymphoma gastric carcinoma invasive ductal breast carcinoma MALT lymphoma ovarian cancer plasma cell myeloma systemic sclerosis Crohn disease exocrine pancreatic carcinoma glioblastoma malignant glioma myositis
B	Pharos: Q96SW2	intellectual disability, autosomal recessive 2 plasma cell myeloma 3p- syndrome intellectual disability toxic or drug-related embryofetopathy central nervous system malformation Erythema nodosum leprosum mantle cell lymphoma non-small cell lung carcinoma follicular lymphoma large cell medulloblastoma marginal zone lymphoma osteosarcoma POEMS syndrome attention deficit hyperactivity disorder, inattentive type intellectual disability, autosomal recessive 2 plasma cell myeloma 3p- syndrome intellectual disability toxic or drug-related embryofetopathy central nervous system malformation Erythema nodosum leprosum mantle cell lymphoma non-small cell lung carcinoma follicular lymphoma large cell medulloblastoma marginal zone lymphoma osteosarcoma POEMS syndrome attention deficit hyperactivity disorder, inattentive type lung adenocarcinoma myelodysplastic syndrome ovarian cancer

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.