Annotations: 9SQV

Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth G]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B [auth H]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G], B [auth H]	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
C, D	PF21125	BRCA1-A complex subunit Abraxas 1 MPN domain (MPN_2A_DUB_like)	BRCA1-A complex subunit Abraxas 1 MPN domain	This entry represents the MPN domain from the Abraxas protein [1-3]. Abraxas is a component of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substra ...	This entry represents the MPN domain from the Abraxas protein [1-3]. Abraxas is a component of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates.	Domain
E [auth A], F [auth B]	PF18110	BRCC36 C-terminal helical domain (BRCC36_C)	BRCC36 C-terminal helical domain	This is the C-terminal domain of BRCC36, a Zn2+ dependent deubiquitinating enzyme, present in Camponotus floridanus. BRCC36 hydrolyzes lysine linked ubiquitin chains as part of macromolecular complexes that participate in either interferon signalling ...	This is the C-terminal domain of BRCC36, a Zn2+ dependent deubiquitinating enzyme, present in Camponotus floridanus. BRCC36 hydrolyzes lysine linked ubiquitin chains as part of macromolecular complexes that participate in either interferon signalling or DNA-damage recognition. The domain consists of 2 non canonical helices. The domain interacts hydrophobically with helices alpha 4 and alpha 5 of KIAA0157 in the form of a coiled coil helical bundle. This interaction helps establish the association of BRCC36 with KIAA0157, a pseudo-DUB MPN- protein that is essential for the activity of BRCC36 [1].	Domain
G [auth F], H [auth E]	PF06113	Brain and reproductive organ-expressed protein (BRE) (BRE)	Brain and reproductive organ-expressed protein (BRE)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G], B [auth H]	Ubiquitin	protein tag activity molecular tag activity RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome	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	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle cytosolic ribosome membraneless organelle intracellular membraneless organelle ribosome cytosol extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
C, D	BRCA1-A complex subunit Abraxas 1	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding polyubiquitin modification-dependent protein binding modification-dependent protein binding	response to ionizing radiation response to stimulus response to radiation response to abiotic stimulus cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition DNA damage checkpoint signaling signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition response to ionizing radiation response to stimulus response to radiation response to abiotic stimulus cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition DNA damage checkpoint signaling signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process DNA damage response negative regulation of cell cycle G2/M phase transition signal transduction in response to DNA damage cellular process negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition metaphase chromosome alignment localization attachment of spindle microtubules to kinetochore chromosome localization organelle localization nuclear chromosome segregation chromosome segregation microtubule cytoskeleton organization membraneless organelle assembly cellular component organization cellular component biogenesis cellular component assembly mitotic sister chromatid segregation cellular component organization or biogenesis microtubule cytoskeleton organization involved in mitosis spindle organization mitotic nuclear division organelle assembly organelle fission chromosome organization sister chromatid segregation spindle assembly mitotic spindle organization mitotic spindle assembly organelle organization nuclear division microtubule-based process cytoskeleton organization double-strand break repair primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair regulation of cellular response to stress regulation of primary metabolic process regulation of response to stress regulation of nucleobase-containing compound metabolic process regulation of macromolecule metabolic process regulation of DNA repair regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process positive regulation of biological process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of DNA metabolic process chromatin organization	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex nuclear protein-containing complex BRCA1-A complex
E [auth A], F [auth B]	Lys-63-specific deubiquitinase BRCC36	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity enzyme regulator activity molecular function regulator activity ubiquitin-like protein peptidase activity metal-dependent deubiquitinase activity deubiquitinase activity K63-linked deubiquitinase activity cysteine-type peptidase activity cysteine-type deubiquitinase activity polyubiquitin modification-dependent protein binding peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity enzyme regulator activity molecular function regulator activity ubiquitin-like protein peptidase activity metal-dependent deubiquitinase activity deubiquitinase activity K63-linked deubiquitinase activity cysteine-type peptidase activity cysteine-type deubiquitinase activity polyubiquitin modification-dependent protein binding protein binding binding modification-dependent protein binding cation binding ion binding metal ion binding small molecule binding	cellular process cell division cellular response to stimulus DNA repair-dependent chromatin remodeling response to stimulus cellular component organization cellular response to stress DNA damage response chromatin organization response to stress chromatin remodeling cellular component organization or biogenesis response to X-ray response to ionizing radiation cellular process cell division cellular response to stimulus DNA repair-dependent chromatin remodeling response to stimulus cellular component organization cellular response to stress DNA damage response chromatin organization response to stress chromatin remodeling cellular component organization or biogenesis response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus cellular response to ionizing radiation cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus regulation of cellular process positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process DNA repair regulation of biological process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process protein deubiquitination protein K63-linked deubiquitination protein modification by small protein removal macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal DNA damage checkpoint signaling regulation of cell cycle phase transition signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition regulation of signal transduction intracellular signal transduction cell communication regulation of cell cycle checkpoint regulation of intracellular signal transduction negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process regulation of signaling regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage regulation of cell communication regulation of DNA damage checkpoint response to nutrient levels response to chemical response to nutrient response to oxygen-containing compound response to vitamin B6 response to nitrogen compound response to vitamin positive regulation of cell communication positive regulation of response to biotic stimulus positive regulation of signal transduction pattern recognition receptor signaling pathway regulation of NLRP3 inflammasome complex assembly positive regulation of NLRP3 inflammasome complex assembly response to biotic stimulus cellular component biogenesis immune response-activating signaling pathway cellular component assembly inflammasome-mediated signaling pathway positive regulation of immune response canonical inflammasome complex assembly regulation of immune system process positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus positive regulation of intracellular signal transduction positive regulation of inflammasome-mediated signaling pathway regulation of inflammasome-mediated signaling pathway defense response to other organism regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly positive regulation of defense response activation of innate immune response regulation of immune response inflammatory response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular component organization positive regulation of cellular component organization regulation of response to external stimulus intracellular receptor signaling pathway regulation of cytoplasmic pattern recognition receptor signaling pathway regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of response to external stimulus immune response-regulating signaling pathway innate immune response protein-containing complex assembly response to external biotic stimulus positive regulation of innate immune response defense response protein-containing complex organization positive regulation of cellular component biogenesis defense response to symbiont regulation of cellular component biogenesis immune system process positive regulation of signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition double-strand break repair proteolysis	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle nucleus intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex nuclear protein-containing complex BRCA1-A complex BRISC complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex nuclear ubiquitin ligase complex
G [auth F], H [auth E]	BRISC and BRCA1-A complex member 2	peroxisome signal sequence receptor activity signal sequence receptor activity polyubiquitin modification-dependent protein binding protein binding binding modification-dependent protein binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell division regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell division regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death response to ionizing radiation cellular response to ionizing radiation response to radiation response to abiotic stimulus cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process DNA repair primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process protein deubiquitination protein K63-linked deubiquitination protein modification by small protein removal macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal DNA damage checkpoint signaling regulation of cell cycle phase transition signaling negative regulation of cell cycle cell cycle phase transition regulation of signal transduction intracellular signal transduction cell communication regulation of cell cycle checkpoint regulation of intracellular signal transduction negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process regulation of signaling regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage regulation of cell communication regulation of DNA damage checkpoint response to nutrient levels response to chemical response to nutrient response to oxygen-containing compound response to vitamin B6 response to nitrogen compound response to vitamin G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition double-strand break repair cellular component organization chromatin organization cellular component organization or biogenesis	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 nuclear protein-containing complex BRCA1-A complex BRISC complex ubiquitin ligase complex catalytic complex transferase complex nuclear ubiquitin ligase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G], B [auth H]	IPR019954	Ubiquitin conserved site	Conserved Site
A [auth G], B [auth H]	IPR000626	Ubiquitin-like domain	Domain
A [auth G], B [auth H]	IPR019956	Ubiquitin domain	Domain
A [auth G], B [auth H]	IPR050158	Ubiquitin and ubiquitin-like	Family
A [auth G], B [auth H]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C, D	IPR023238	FAM175 family	Family
C, D	IPR023239	BRISC complex, Abraxas 1 subunit	Family
C, D	IPR037518	MPN domain	Domain
E [auth A], F [auth B]	IPR033860	Brcc36 isopeptidase	Family
E [auth A], F [auth B]	IPR050242	JAMM/MPN+ metalloenzymes, peptidase M67A	Family
E [auth A], F [auth B]	IPR037518	MPN domain	Domain
E [auth A], F [auth B]	IPR040749	BRCC36, C-terminal helical domain	Domain
E [auth A], F [auth B]	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain
G [auth F], H [auth E]	IPR010358	BRCA1-A complex subunit BRE	Family

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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.

9SQV | pdb_00009sqv

Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage