6CRN

Structure of the USP15 deubiquitinase domain in complex with a high-affinity first-generation Ubv

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6crna1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6crna2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6crnb_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6crnc_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6crnd1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6crnd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6crne_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6crnf_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6crng_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6crnh_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	UCH	e6crnA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
B	UCH	e6crnB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
C	UCH	e6crnC1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
D	UCH	e6crnD1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: UCH	ECOD (1.6)
E	ubiquitin_1	e6crnE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
F	ubiquitin_1	e6crnF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
G	ubiquitin_1	e6crnG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
H	ubiquitin_1	e6crnH1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
B	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
C	3.90.70.10	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
D	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, B, C, D	PF00443	Ubiquitin carboxyl-terminal hydrolase (UCH)	Ubiquitin carboxyl-terminal hydrolase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Ubiquitin carboxyl-terminal hydrolase 15	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 transforming growth factor beta receptor binding protein binding binding signaling receptor 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 transforming growth factor beta receptor binding protein binding binding signaling receptor binding cytokine receptor binding cysteine-type deubiquitinase activity SMAD binding ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity modification-dependent protein binding protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity identical protein binding	cellular response to stimulus cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell communication cellular response to endogenous stimulus response to BMP cellular response to stimulus cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell communication cellular response to endogenous stimulus response to BMP cellular process transforming growth factor beta receptor superfamily signaling pathway signal transduction response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway protein deubiquitination organonitrogen compound metabolic process primary metabolic process monoubiquitinated protein deubiquitination 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 regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of biological process response to biotic stimulus negative regulation of antifungal innate immune response response to stress regulation of response to stress innate immune response regulation of antifungal innate immune response regulation of immune system process response to external biotic stimulus antifungal innate immune response immune response response to other organism defense response negative regulation of response to stimulus regulation of innate immune response negative regulation of immune response defense response to symbiont response to external stimulus defense response to fungus regulation of defense response to fungus regulation of response to stimulus negative regulation of immune system process immune system process defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response response to fungus negative regulation of innate immune response positive regulation of cell communication positive regulation of response to biotic stimulus positive regulation of signal transduction pattern recognition receptor signaling pathway regulation of signal transduction immune response-activating signaling pathway positive regulation of immune response positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway regulation of RIG-I signaling pathway RIG-I signaling pathway regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response positive regulation of RIG-I signaling pathway activation of immune response cytoplasmic pattern recognition receptor signaling pathway intracellular receptor signaling pathway positive regulation of biological process regulation of cytoplasmic pattern recognition receptor signaling pathway positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of cellular process regulation of signaling positive regulation of innate immune response regulation of cell communication positive regulation of signaling protein K27-linked deubiquitination negative regulation of transforming growth factor beta receptor signaling pathway negative regulation of signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of cell communication regulation of transforming growth factor beta receptor signaling pathway negative regulation of cellular process regulation of cellular response to transforming growth factor beta stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction response to transforming growth factor beta transforming growth factor beta receptor signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway transcription elongation by RNA polymerase II cellular biosynthetic process RNA metabolic process protein-DNA complex organization cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II chromatin organization organic substance biosynthetic process chromatin remodeling cellular component organization or biogenesis transcription elongation-coupled chromatin remodeling protein-containing complex organization cellular metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process DNA-templated transcription elongation biosynthetic process organic cyclic compound biosynthetic process intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator regulation of cellular response to stress cellular response to chemical stress regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cellular response to environmental stimulus regulation of response to osmotic stress regulation of cellular response to osmotic stress cellular response to stress regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator intrinsic apoptotic signaling pathway response to osmotic stress regulation of apoptotic process regulation of intrinsic apoptotic signaling pathway in response to osmotic stress regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator signal transduction by p53 class mediator cellular response to osmotic stress cell death apoptotic signaling pathway cellular response to chemical stimulus intrinsic apoptotic signaling pathway in response to osmotic stress response to chemical response to abiotic stimulus intrinsic apoptotic signaling pathway by p53 class mediator cellular response to abiotic stimulus apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death regulation of apoptotic signaling pathway proteolysis	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear body
E, F, G, H	Ubiquitin variant 15.2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR028889	Ubiquitin specific protease domain	Domain
A, B, C, D	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, B, C, D	IPR006615	Peptidase C19, ubiquitin-specific peptidase, DUSP domain	Domain
A, B, C, D	IPR013792	RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta	Homologous Superfamily
A, B, C, D	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D	IPR029346	Ubiquitin carboxyl-terminal hydrolase, C-terminal	Domain
A, B, C, D	IPR028135	Ubiquitin-like domain, USP-type	Domain
A, B, C, D	IPR035927	DUSP-like superfamily	Homologous Superfamily
A, B, C, D	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, B, C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9Y4E8	atopic eczema hereditary spastic paraplegia lymphoplasmacytic lymphoma malignant mesothelioma ovarian cancer transitional cell carcinoma atypical teratoid rhabdoid tumor large cell medulloblastoma malignant ependymoma medulloblastoma pilocytic astrocytoma glioblastoma lung cancer malignant glioma osteosarcoma atopic eczema hereditary spastic paraplegia lymphoplasmacytic lymphoma malignant mesothelioma ovarian cancer transitional cell carcinoma atypical teratoid rhabdoid tumor large cell medulloblastoma malignant ependymoma medulloblastoma pilocytic astrocytoma glioblastoma lung cancer malignant glioma osteosarcoma primitive neuroectodermal tumor

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.