5CVO

WDR48:USP46~ubiquitin ternary complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	SCOP2B Superfamily	Cysteine proteinases	8067281	3001808	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cysteine proteinases	8067281	3001808	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8101457	3000157	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00400	e5cvoA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
A	F_UNCLASSIFIED	e5cvoA2	A: beta duplicates or obligate multimers	X: WD repeat-containing protein 48 ancillary domain (From Topology)	H: WD repeat-containing protein 48 ancillary domain (From Topology)	T: WD repeat-containing protein 48 ancillary domain	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF00443	e5cvoB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00443	ECOD (1.6)
E	PF00443	e5cvoE1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF00443	ECOD (1.6)
C	PF00240	e5cvoC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
F	PF00240	e5cvoF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
E	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF11816	Domain of unknown function (DUF3337) (DUF3337)	Domain of unknown function (DUF3337)	-	Family
A, D	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
B, E	PF00443	Ubiquitin carboxyl-terminal hydrolase (UCH)	Ubiquitin carboxyl-terminal hydrolase	-	Family
C, F	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	WD repeat-containing protein 48	protein binding binding ubiquitin binding ubiquitin-like protein binding DNA binding organic cyclic compound binding nucleic acid binding double-stranded DNA binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity deubiquitinase activator activity protein binding binding ubiquitin binding ubiquitin-like protein binding DNA binding organic cyclic compound binding nucleic acid binding double-stranded DNA binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity deubiquitinase activator activity peptidase activator activity single-stranded DNA 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 reproductive system development gonad development tube development reproductive process sex differentiation animal organ development cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development anatomical structure development reproductive structure development system development spermatogenesis sexual reproduction multicellular organismal reproductive process male gamete generation gamete generation multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells skin development fertilization single fertilization regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation positive regulation of epithelial cell proliferation biological regulation positive regulation of biological process regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of cellular process embryonic organ development embryo development regulation of DNA recombination regulation of double-strand break repair regulation of cellular response to stress positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process organic substance metabolic process positive regulation of DNA repair regulation of response to stress recombinational repair positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination DNA repair positive regulation of DNA recombination double-strand break repair positive regulation of nucleobase-containing compound metabolic process DNA recombination primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair regulation of double-strand break repair via homologous recombination organic cyclic compound metabolic process 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 positive regulation of cell communication cell surface receptor signaling pathway via STAT positive regulation of signal transduction signaling positive regulation of receptor signaling pathway via STAT regulation of signal transduction positive regulation of receptor signaling pathway via JAK-STAT cell communication regulation of receptor signaling pathway via JAK-STAT signal transduction regulation of signaling cell surface receptor signaling pathway regulation of cell communication regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT positive regulation of signaling anatomical structure morphogenesis skeletal system development skeletal system morphogenesis animal organ morphogenesis regulation of protein modification process regulation of protein ubiquitination protein ubiquitination protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process organonitrogen compound metabolic process regulation of post-translational protein modification regulation of protein metabolic process protein monoubiquitination macromolecule modification regulation of protein monoubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal multicellular organism growth developmental growth growth	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen lytic vacuole vacuole lysosome endosome intracellular vesicle endomembrane system cytoplasmic vesicle late endosome vesicle
B, E	Ubiquitin carboxyl-terminal hydrolase 46	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity cation binding ion binding binding metal ion binding small molecule binding	trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process synaptic transmission, GABAergic modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process synaptic transmission, GABAergic modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication cellular process regulation of synaptic transmission, GABAergic reflex response to stimulus response to external stimulus righting reflex behavioral defense response behavior multicellular organismal process fear response behavioral fear response defense response response to stress multicellular organismal response to stress protein deubiquitination organonitrogen compound metabolic process primary metabolic process organic substance metabolic process protein modification by small protein removal macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation or removal proteolysis adult feeding behavior adult behavior feeding behavior response to organic substance response to alcohol response to chemical behavioral response to ethanol response to oxygen-containing compound response to ethanol	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
C, F	Polyubiquitin-B	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding	developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development developmental process multicellular organismal process reproductive system development gonad development tube development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics seminiferous tubule development anatomical structure development reproductive structure development system development regulation of mitochondrial membrane potential biological regulation regulation of biological quality regulation of membrane potential organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process regulation of biological process neuron apoptotic process regulation of cellular process regulation of apoptotic process regulation of programmed cell death cell death cellular process apoptotic process programmed cell death regulation of neuron apoptotic process multicellular organismal-level homeostasis homeostatic process energy homeostasis 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 protein ubiquitination positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal protein modification 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 macromolecule modification post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction intrinsic apoptotic signaling pathway positive regulation of cellular process regulation of signaling positive regulation of programmed cell death positive regulation of intracellular signal transduction signal transduction by p53 class mediator positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway positive regulation of signaling cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation brain development diencephalon development forebrain neuron development central nervous system development forebrain neuron differentiation sexual reproduction organelle fission meiotic cell cycle multicellular organismal reproductive process female gamete generation meiotic cell cycle process gamete generation nuclear division organelle organization meiosis I meiosis I cell cycle process female meiosis I female meiotic nuclear division meiotic nuclear division cell cycle cell cycle process positive regulation of protein monoubiquitination protein monoubiquitination regulation of protein monoubiquitination regulation of proteolysis involved in protein catabolic process regulation of proteolysis proteasomal protein catabolic process regulation of catabolic process regulation of proteasomal protein catabolic process regulation of protein catabolic process male meiosis I male meiotic nuclear division male gamete generation connective tissue development adipose tissue development fat pad development tissue development female gonad development female sex differentiation development of primary female sexual characteristics establishment of organelle localization cellular localization organelle transport along microtubule transport establishment of mitochondrion localization intracellular transport establishment of localization localization mitochondrion localization establishment of mitochondrion localization, microtubule-mediated mitochondrion transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cell projection neuron projection plasma membrane bounded cell projection intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane endocytic vesicle endosome membrane endosome mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane somatodendritic compartment cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR019775	WD40 repeat, conserved site	Conserved Site
A, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, D	IPR021772	WDR48/Bun107	Family
A, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, D	IPR001680	WD40 repeat	Repeat
A, D	IPR020472	G-protein beta WD-40 repeat	Repeat
B, E	IPR028889	Ubiquitin specific protease domain	Domain
B, E	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
B, E	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
B, E	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
C, F	IPR019954	Ubiquitin conserved site	Conserved Site
C, F	IPR000626	Ubiquitin-like domain	Domain
C, F	IPR019956	Ubiquitin domain	Domain
C, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D	Pharos: Q8TAF3	malignant mesothelioma osteosarcoma Spastic Paraplegia, Hereditary medulloblastoma ovarian cancer metabolic syndrome X psoriasis
B, E	Pharos: P62068	atypical teratoid rhabdoid tumor glioblastoma lung cancer malignant glioma osteosarcoma primitive neuroectodermal tumor subependymal giant cell astrocytoma bipolar disorder interstitial cystitis major depressive disorder medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia cystic fibrosis large cell medulloblastoma atypical teratoid rhabdoid tumor glioblastoma lung cancer malignant glioma osteosarcoma primitive neuroectodermal tumor subependymal giant cell astrocytoma bipolar disorder interstitial cystitis major depressive disorder medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia cystic fibrosis large cell medulloblastoma malignant ependymoma non-small cell lung carcinoma pituitary cancer spina bifida
C, F	Pharos: P0CG47	astrocytic tumor cleft soft palate lung cancer Cleft of hard palate ovarian cancer isolated cleft palate

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 R01GM133198.