9PTU | pdb_00009ptu

Cryo-EM structure of the DCAF11 E3 ligase bound to the DDX18 helicase mediated by GSH-M12

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)
C [auth B]	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	WD40 repeat-like	8052530	3001694	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	WD40 repeat-like	8051194	3001694	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B]	PF10433	RSE1/DDB1/CPSF1 first beta-propeller (Beta-prop_RSE1_1st)	RSE1/DDB1/CPSF1 first beta-propeller	-	Repeat
C [auth B]	PF03178	CPSF A subunit region (CPSF_A)	CPSF A subunit region	-	Repeat
B [auth C]	PF13959	ATP-dependent rRNA helicase SPB4-like, C-terminal extension (CTE_SPB4)	ATP-dependent rRNA helicase SPB4-like, C-terminal extension	This short domain is found at the C-terminus of many helicase proteins, including ATP-dependent rRNA helicase SPB4 from Saccharomyces cerevisiae, which is involved in the biogenesis of 60S ribosomal subunits. SPB4 is organised into four domains: dual ...	This short domain is found at the C-terminus of many helicase proteins, including ATP-dependent rRNA helicase SPB4 from Saccharomyces cerevisiae, which is involved in the biogenesis of 60S ribosomal subunits. SPB4 is organised into four domains: dual RecA domains (Pfam:PF00270 and Pfam:PF00271), a C-terminal extension (CTE, represented by this entry) and a C-terminal tail (Pfam:PF23681). This domain packs closely onto the catalytic core and engages the four nucleotides immediately 5' to those within the RNA binding pocket. It shows a mainly alpha- helical structure [1].	Domain
B [auth C]	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
A	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 C]	ATP-dependent RNA helicase DDX18	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 pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity RNA binding nucleic acid binding	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process ribosomal large subunit biogenesis macromolecule biosynthetic process nucleic acid metabolic process maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biosynthetic process cellular process metabolic process macromolecule metabolic process maturation of LSU-rRNA cellular response to stimulus response to lipid response to stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to lipid response to estradiol cellular response to estradiol stimulus	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 chromosome
A	DDB1- and CUL4-associated factor 11	-	regulation of cytokinesis regulation of biological process regulation of cellular process cytoskeleton-dependent cytokinesis regulation of cell cycle process biological regulation mitotic cytokinesis cytokinesis mitotic cell cycle regulation of cell division regulation of mitotic cytokinesis mitotic cell cycle process cellular process cell division regulation of cytokinesis regulation of biological process regulation of cellular process cytoskeleton-dependent cytokinesis regulation of cell cycle process biological regulation mitotic cytokinesis cytokinesis mitotic cell cycle regulation of cell division regulation of mitotic cytokinesis mitotic cell cycle process cellular process cell division cell cycle regulation of cell cycle cell cycle process 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 cellular response to stimulus response to stimulus regulation of cellular response to stress cellular response to stress regulation of response to stimulus regulation of response to stress response to stress 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	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cullin-RING ubiquitin ligase complex protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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 C]	IPR001650	Helicase, C-terminal domain-like	Domain
B [auth C]	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
B [auth C]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
B [auth C]	IPR044773	DDX18/Has1, DEAD-box helicase domain	Domain
B [auth C]	IPR025313	ATP-dependent rRNA helicase SPB4-like, C-terminal extension	Domain
B [auth C]	IPR011545	DEAD/DEAH-box helicase domain	Domain
B [auth C]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
A	IPR051859	DDB1- and CUL4-associated factor	Family
A	IPR001680	WD40 repeat	Repeat
A	IPR017399	WD repeat protein DCAF11/LEC14B	Family
A	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth B]	: Q16531	Disease Exacerbation gastric cancer lung cancer xeroderma pigmentosum gastric neoplasm drug-induced liver injury hereditary diffuse gastric adenocarcinoma psoriasis
B [auth C]	: Q9NVP1	dermatomyositis Malignant neoplasm of breast osteosarcoma psoriasis glioblastoma medulloblastoma ovarian cancer large cell medulloblastoma myopathy primitive neuroectodermal tumor
A	: Q8TEB1	dermatomyositis osteosarcoma pancreatic ductal adenocarcinoma

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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.