6DJ9 | pdb_00006dj9

Structure of the USP15 DUSP domain in complex with a high-affinity Ubiquitin Variant (UbV)

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L	d6dj9l_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d6dj9k_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d6dj9j_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d6dj9i_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6dj9h_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6dj9g_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6dj9f_	Alpha and beta proteins (a+b)	DUSP-like	DUSP-like	DUSP, domain in ubiquitin-specific proteases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d6dj9e_	Alpha and beta proteins (a+b)	DUSP-like	DUSP-like	DUSP, domain in ubiquitin-specific proteases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6dj9d_	Alpha and beta proteins (a+b)	DUSP-like	DUSP-like	DUSP, domain in ubiquitin-specific proteases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6dj9c_	Alpha and beta proteins (a+b)	DUSP-like	DUSP-like	DUSP, domain in ubiquitin-specific proteases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6dj9b_	Alpha and beta proteins (a+b)	DUSP-like	DUSP-like	DUSP, domain in ubiquitin-specific proteases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6dj9a_	Alpha and beta proteins (a+b)	DUSP-like	DUSP-like	DUSP, domain in ubiquitin-specific proteases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	DUSP-like	8032908	3001970	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DUSP-like	8032908	3001970	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DUSP-like	8032908	3001970	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DUSP-like	8032908	3001970	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DUSP-like	8032908	3001970	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DUSP-like	8032908	3001970	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)
L		e6dj9L1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: C1-set	F:	ECOD (20:10:01)
K		e6dj9K1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: C1-set	F:	ECOD (20:10:01)
J		e6dj9J1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: C1-set	F:	ECOD (20:10:01)
I		e6dj9I1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: C1-set	F:	ECOD (20:10:01)
H		e6dj9H1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: zf-B_box	F:	ECOD (20:10:01)
G		e6dj9G1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: C1-set	F:	ECOD (20:10:01)
F		e6dj9F1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: zf-B_box	F:	ECOD (20:10:01)
E		e6dj9E1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: DNA_gyraseB_C,Toprim	F:	ECOD (20:10:01)
D		e6dj9D1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: DNA_gyraseB_C,Toprim	F:	ECOD (20:10:01)
C		e6dj9C1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: DNA_gyraseB_C,Toprim	F:	ECOD (20:10:01)
B		e6dj9B1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: DNA_gyraseB_C,Toprim	F:	ECOD (20:10:01)
A		e6dj9A1	A: PriB N-terminal domain-like	X: Rubredoxin-related	H: Aconitase iron-sulfur domain	T: C1-set	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.30.2230.10	Alpha Beta	2-Layer Sandwich	DUSP-like	DUSP-like	CATH (utative)
D	3.30.2230.10	Alpha Beta	2-Layer Sandwich	DUSP-like	DUSP-like	CATH (utative)
C	3.30.2230.10	Alpha Beta	2-Layer Sandwich	DUSP-like	DUSP-like	CATH (utative)
A	3.30.2230.10	Alpha Beta	2-Layer Sandwich	DUSP-like	DUSP-like	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF06337	DUSP domain (DUSP)	DUSP domain	The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved [1]. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporti ...	The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved [1]. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, J, K G, H, I, J, K, L	Ubiquitin Variant UbV 15.D	-	-	-
A, B, C, D, E A, B, C, D, E, F	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 ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity K48-linked deubiquitinase activity catalytic activity deubiquitinase activity ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor 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 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 RNA metabolic process primary metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process metabolic process regulation of nucleobase-containing compound metabolic process macromolecule metabolic process regulation of metabolic process protein deubiquitination monoubiquitinated protein 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 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 intracellular 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 positive regulation of intracellular signal transduction 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 regulation of intracellular signal transduction 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 transcription elongation-coupled chromatin remodeling nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process cellular component organization RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II biosynthetic process chromatin organization chromatin remodeling cellular component organization or biogenesis 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 cellular response to environmental stimulus regulation of response to osmotic stress regulation of cellular response to osmotic stress cellular response to stress 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen intracellular membraneless organelle nuclear body membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR006615	Peptidase C19, ubiquitin-specific peptidase, DUSP domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013792	RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR050185	Ubiquitin carboxyl-terminal hydrolase	Family
A, B, C, D, E A, B, C, D, E, F	IPR029346	Ubiquitin carboxyl-terminal hydrolase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR028135	Ubiquitin-like domain, USP-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR035927	DUSP-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	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 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.