9PLR | pdb_00009plr

CryoEM reconstruction of HUWE1-USP7 complex in the closed state

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)
B [auth C]	SCOP2B Superfamily	Cysteine proteinases	8043739	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Hect, E3 ligase catalytic domain	8084363	3000934	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	PF22486	MATH domain (MATH_2)	MATH domain	This motif has been called the Meprin And TRAF-Homology (MATH) domain.ED A0A835B747.1/23-123; A0A835B747.1/23-76;	Domain
B [auth C]	PF14533	Ubiquitin-specific protease C-terminal (USP7_C2)	Ubiquitin-specific protease C-terminal	-	Family
B [auth C]	PF00443	Ubiquitin carboxyl-terminal hydrolase (UCH)	Ubiquitin carboxyl-terminal hydrolase	-	Family
B [auth C]	PF12436	ICP0-binding domain of Ubiquitin-specific protease 7 (USP7_ICP0_bdg)	ICP0-binding domain of Ubiquitin-specific protease 7	-	Family
A	PF02825	WWE domain (WWE)	WWE domain	The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems [1].	Domain
A	PF06025	Domain of Unknown Function (DUF913) (DUF913)	Domain of Unknown Function (DUF913)	-	Family
A	PF06012	Domain of Unknown Function (DUF908) (DUF908)	Domain of Unknown Function (DUF908)	-	Family
A	PF00632	HECT-domain (ubiquitin-transferase) (HECT)	HECT-domain (ubiquitin-transferase)	The name HECT comes from Homologous to the E6-AP Carboxyl Terminus.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	Ubiquitin carboxyl-terminal hydrolase 7	p53 binding protein binding binding ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity K48-linked deubiquitinase activity catalytic activity deubiquitinase activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity cysteine-type deubiquitinase activity	regulation of protein stability biological regulation regulation of biological quality protein stabilization regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of protein stability biological regulation regulation of biological quality protein stabilization regulation of cellular process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression negative regulation of metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process rhythmic process circadian rhythm regulation of circadian rhythm regulation of localization cellular localization regulation of transport transport intracellular transport regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport endosomal transport localization regulation of cellular localization cytosolic transport establishment of localization in cell retrograde transport, endosome to Golgi regulation of retrograde transport, endosome to Golgi regulation of intracellular transport primary metabolic process protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal protein deubiquitination monoubiquitinated protein deubiquitination protein modification by small protein removal cellular response to stimulus response to stimulus DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA alkylation repair cellular response to stress DNA damage response response to stress DNA repair transcription-coupled nucleotide-excision repair nucleotide-excision repair catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process negative regulation of protein catabolic process modification-dependent macromolecule catabolic process negative regulation of protein metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process establishment of protein localization to telomere establishment of protein localization regulation of protein localization regulation of establishment of protein localization establishment of protein localization to organelle regulation of establishment of protein localization to telomere macromolecule localization establishment of protein localization to chromosome intracellular protein localization regulation of establishment of protein localization to chromosome biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus immune system process defense response to other organism innate immune response antiviral innate immune response response to external biotic stimulus response to virus symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cell PML body disruption of anatomical structure in another organism symbiont-mediated disruption of host cellular anatomical structure regulation of telomere maintenance regulation of cellular component organization telomere organization regulation of nucleobase-containing compound metabolic process chromosome organization regulation of chromosome organization regulation of organelle organization telomere maintenance organelle organization telomere capping regulation of telomere capping regulation of DNA metabolic process signaling negative regulation of signaling negative regulation of intracellular signal transduction 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 signal transduction regulation of TORC1 signaling TOR signaling regulation of signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication TORC1 signaling monosaccharide metabolic process negative regulation of small molecule metabolic process gluconeogenesis negative regulation of gluconeogenesis regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process negative regulation of carbohydrate metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process regulation of gluconeogenesis regulation of carbohydrate biosynthetic process glucose metabolic process signal transduction by p53 class mediator regulation of signal transduction by p53 class mediator response to cytokine cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus regulation of tumor necrosis factor-mediated signaling pathway cell surface receptor signaling pathway regulation of cytokine-mediated signaling pathway response to peptide regulation of response to cytokine stimulus response to chemical response to tumor necrosis factor proteolysis	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 membraneless organelle intracellular membraneless organelle chromosome nuclear body PML body
A	E3 ubiquitin-protein ligase HUWE1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity RNA binding binding nucleic acid binding DNA binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-ubiquitin ligase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity RNA binding binding nucleic acid binding DNA binding histone ubiquitin ligase activity histone modifying activity	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling protein polyubiquitination protein branched polyubiquitination 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 developmental process cellular developmental process cell differentiation regulation of cellular component organization regulation of developmental process negative regulation of mitochondrial fusion negative regulation of biological process negative regulation of cellular process anatomical structure development regulation of mitochondrial fusion mitochondrial fusion regulation of anatomical structure morphogenesis mitochondrion organization negative regulation of cellular component organization negative regulation of developmental process regulation of organelle organization organelle fusion anatomical structure morphogenesis organelle organization negative regulation of organelle organization regulation of mitochondrion organization regulation of protein modification process positive regulation of protein metabolic 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 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 catabolic process regulation of type 2 mitophagy macroautophagy positive regulation of type 2 mitophagy autophagy regulation of autophagy positive regulation of autophagy of mitochondrion mitophagy regulation of autophagy of mitochondrion positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of autophagy positive regulation of mitophagy regulation of mitophagy regulation of catabolic process positive regulation of catabolic process regulation of macroautophagy type 2 mitophagy autophagy of mitochondrion 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 regulation of biosynthetic process rhythmic process circadian regulation of gene expression circadian rhythm gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process protein K48-linked ubiquitination DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair cellular response to stress DNA damage response response to stress DNA repair intracellular receptor signaling pathway negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of cell communication negative regulation of response to stimulus negative regulation of signal transduction peroxisome proliferator activated receptor signaling pathway regulation of peroxisome proliferator activated receptor signaling pathway nuclear receptor-mediated signaling pathway negative regulation of peroxisome proliferator activated receptor signaling pathway protein monoubiquitination Golgi organization endomembrane system organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane nuclear membrane nucleus endomembrane system organelle envelope nuclear envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane nuclear membrane nucleus endomembrane system organelle envelope nuclear envelope organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular organelle lumen organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle nucleoplasm nuclear lumen Golgi membrane Golgi apparatus bounding membrane of organelle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
B [auth C]	IPR024729	Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain	Domain
B [auth C]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
B [auth C]	IPR002083	MATH/TRAF domain	Domain
B [auth C]	IPR029346	Ubiquitin carboxyl-terminal hydrolase, C-terminal	Domain
B [auth C]	IPR050164	Ubiquitin carboxyl-terminal hydrolases	Family
B [auth C]	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
B [auth C]	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
B [auth C]	IPR008974	TRAF-like	Homologous Superfamily
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR041918	HUWE1, UBA domain	Domain
A	IPR010309	E3 ubiquitin ligase, domain of unknown function DUF908	Domain
A	IPR035983	HECT, E3 ligase catalytic domain	Homologous Superfamily
A	IPR050409	E3 ubiquitin-protein ligase	Family
A	IPR015940	Ubiquitin-associated domain	Domain
A	IPR000569	HECT domain	Domain
A	IPR010314	E3 ubiquitin ligase, domain of unknown function DUF913	Domain
A	IPR025527	HUWE1/REV1, ubiquitin-binding motif	Conserved Site
A	IPR004170	WWE domain	Domain
A	IPR037197	WWE domain superfamily	Homologous Superfamily
A	IPR009060	UBA-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C]	: Q93009	urinary bladder cancer prostate cancer Hao-Fountain syndrome Prostatic Neoplasms intellectual disability urinary bladder neoplasm
A	: Q7Z6Z7	intellectual disability, X-linked syndromic, Turner type Mental retardation, X-linked, syndromic, Turner type intellectual disability astrocytic tumor craniosynostosis malignant glioma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma primitive neuroectodermal tumor chromosome Xp11.22 duplication syndrome intellectual disability, X-linked syndromic, Turner type Mental retardation, X-linked, syndromic, Turner type intellectual disability astrocytic tumor craniosynostosis malignant glioma pilocytic astrocytoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma primitive neuroectodermal tumor chromosome Xp11.22 duplication syndrome malignant ependymoma ovarian cancer psoriasis

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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.