2GWF | pdb_00002gwf

Structure of a USP8-NRDP1 complex

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)
F	d2gwff_	Alpha and beta proteins (a+b)	NRDP1 C-terminal domain-like	NRDP1 C-terminal domain-like	USP8 interacting domain	E3 ubiquitin-protein ligase NRDP1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2gwfd2	Alpha and beta proteins (a+b)	NRDP1 C-terminal domain-like	NRDP1 C-terminal domain-like	USP8 interacting domain	E3 ubiquitin-protein ligase NRDP1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2gwfd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2gwfb1	Alpha and beta proteins (a+b)	NRDP1 C-terminal domain-like	NRDP1 C-terminal domain-like	USP8 interacting domain	E3 ubiquitin-protein ligase NRDP1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2gwfe2	Alpha and beta proteins (a/b)	Rhodanese/Cell cycle control phosphatase	Rhodanese/Cell cycle control phosphatase	Ubiquitin carboxyl-terminal hydrolase 8, USP8	Ubiquitin carboxyl-terminal hydrolase 8, USP8	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2gwfe3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2gwfc2	Alpha and beta proteins (a/b)	Rhodanese/Cell cycle control phosphatase	Rhodanese/Cell cycle control phosphatase	Ubiquitin carboxyl-terminal hydrolase 8, USP8	Ubiquitin carboxyl-terminal hydrolase 8, USP8	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2gwfc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2gwfa2	Alpha and beta proteins (a/b)	Rhodanese/Cell cycle control phosphatase	Rhodanese/Cell cycle control phosphatase	Ubiquitin carboxyl-terminal hydrolase 8, USP8	Ubiquitin carboxyl-terminal hydrolase 8, USP8	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2gwfa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	NRDP1 C-terminal domain-like	8034011	3000316	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	NRDP1 C-terminal domain-like	8034011	3000316	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	NRDP1 C-terminal domain-like	8034011	3000316	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Rhodanese/Cell cycle control phosphatase	8042088	3000320	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Rhodanese/Cell cycle control phosphatase	8042088	3000320	SCOP2B (2022-06-29)
A	SCOP2 Family	Ubiquitin carboxyl-terminal hydrolase 8, USP8	8029709	4003459	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Rhodanese/Cell cycle control phosphatase	8042088	3000320	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F		e2gwfF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
D		e2gwfD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
B		e2gwfB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
E		e2gwfE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_1	F:	ECOD (20:10:01)
C		e2gwfC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: NAD_binding_1	F:	ECOD (20:10:01)
A		e2gwfA1	A: Flavodoxin-like	X: Flavoproteins/Phosphotyrosine protein phosphatases-like	H: Rhodanese/Cell cycle control phosphatase	T: Rhodanese	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.40.250.10	Alpha Beta	3-Layer(aba) Sandwich	Oxidized Rhodanese	domain 1	CATH (4.3.0)
C	3.40.250.10	Alpha Beta	3-Layer(aba) Sandwich	Oxidized Rhodanese	domain 1	CATH (4.3.0)
A	3.40.250.10	Alpha Beta	3-Layer(aba) Sandwich	Oxidized Rhodanese	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F	PF08941	USP8 interacting (USP8_interact)	USP8 interacting	This domain interacts with the UBP deubiquitinating enzyme USP8.	Domain
A, C, E	PF00581	Rhodanese-like domain (Rhodanese)	Rhodanese-like domain	Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	RING finger protein 41	small GTPase binding protein binding binding enzyme binding GTPase binding protein domain specific binding signaling receptor binding cytokine receptor binding erythropoietin receptor binding interleukin-3 receptor binding growth factor receptor binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein small GTPase binding protein binding binding enzyme binding GTPase binding protein domain specific binding signaling receptor binding cytokine receptor binding erythropoietin receptor binding interleukin-3 receptor binding growth factor receptor binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding	catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion catabolic process regulation of cellular process macroautophagy autophagy negative regulation of biological process regulation of autophagy mitophagy negative regulation of cellular process regulation of autophagy of mitochondrion process utilizing autophagic mechanism negative regulation of catabolic process regulation of biological process negative regulation of metabolic process negative regulation of autophagy of mitochondrion biological regulation regulation of mitophagy regulation of catabolic process negative regulation of mitophagy negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy cellular process metabolic process regulation of metabolic process autophagy of mitochondrion proteasomal protein catabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process cellular response to stimulus regulation of signaling response to stimulus signaling regulation of signal transduction regulation of MAPK cascade intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette MAPK cascade regulation of cell communication signal transduction protein autoubiquitination 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 cell surface receptor signaling pathway cell death extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death positive regulation of protein metabolic process positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of protein metabolic process regulation of macromolecule metabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process developmental process multicellular organismal process regulation of multicellular organismal development regulation of developmental process cellular developmental process regulation of myeloid cell differentiation hemopoiesis cell development regulation of cell differentiation regulation of cell development multicellular organism development myeloid cell differentiation cell differentiation immune system process anatomical structure development regulation of hemopoiesis regulation of immune system process regulation of multicellular organismal process regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation regulation of lymphocyte differentiation cell activation leukocyte differentiation regulation of lymphocyte activation protein polyubiquitination negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle organelle subcompartment intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle endoplasmic reticulum endoplasmic reticulum tubular network perinuclear region of cytoplasm
A, C, E	Ubiquitin carboxyl-terminal hydrolase 8	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 K63-linked deubiquitinase activity SH3 domain 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 K63-linked deubiquitinase activity SH3 domain binding protein binding binding protein domain specific binding cysteine-type deubiquitinase activity cell adhesion molecule binding cadherin binding	mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cellular process cytokinesis cell division cell cycle mitotic cell cycle cell cycle process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of amyloid fibril formation positive regulation of protein metabolic process mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cellular process cytokinesis cell division cell cycle mitotic cell cycle cell cycle process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of amyloid fibril formation positive regulation of protein metabolic process positive regulation of biological process regulation of amyloid fibril formation amyloid fibril formation regulation of primary metabolic process cellular component organization positive regulation of metabolic process positive regulation of macromolecule metabolic process cellular component organization or biogenesis protein metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process positive regulation of supramolecular fiber organization regulation of supramolecular fiber organization metabolic process macromolecule metabolic process supramolecular fiber organization regulation of metabolic process cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor protein deubiquitination protein K63-linked deubiquitination protein modification by small protein removal macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation or removal cellular response to stimulus response to ketone response to lipid response to hormone response to steroid hormone cellular response to ketone cellular response to steroid hormone stimulus cellular response to hormone stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to chemical stimulus response to chemical cellular response to lipid response to dexamethasone small GTPase-mediated signal transduction signaling Ras protein signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction catabolic process modulation of chemical synaptic transmission macromolecule catabolic process regulation of protein catabolic process at postsynapse, modulating synaptic transmission synaptic signaling postsynaptic modulation of chemical synaptic transmission trans-synaptic signaling regulation of signaling cell-cell signaling protein catabolic process regulation of catabolic process chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of protein catabolic process regulation of protein stability regulation of biological quality protein K48-linked deubiquitination regulation of localization localization regulation of protein localization macromolecule localization intracellular protein localization regulation of protein catabolic process in the vacuole negative regulation of biological process lysosomal protein catabolic process negative regulation of protein catabolic process in the vacuole negative regulation of protein catabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process protein catabolic process in the vacuole negative regulation of metabolic process negative regulation of lysosomal protein catabolic process regulation of lysosomal protein catabolic process positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus positive regulation of signaling proteolysis vesicle organization organelle organization endosome organization endomembrane system organization	midbody cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane synapse cell junction glutamatergic synapse membrane-bounded organelle early endosome endosome midbody cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane synapse cell junction glutamatergic synapse membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization asymmetric synapse endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane acrosomal vesicle acrosomal membrane secretory granule secretory vesicle secretory granule membrane nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR013010	Zinc finger, SIAH-type	Domain
B, D, F	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
B, D, F	IPR015036	E3 ubiquitin-protein ligase NRDP1	Domain
B, D, F	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B, D, F	IPR037255	NRDP1, C-terminal	Homologous Superfamily
B, D, F	IPR001841	Zinc finger, RING-type	Domain
A, C, E	IPR048498	USP8, WW domain	Domain
A, C, E	IPR001763	Rhodanese-like domain	Domain
A, C, E	IPR018200	Ubiquitin specific protease, conserved site	Conserved Site
A, C, E	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, C, E	IPR050185	Ubiquitin carboxyl-terminal hydrolase	Family
A, C, E	IPR036873	Rhodanese-like domain superfamily	Homologous Superfamily
A, C, E	IPR015063	USP8 dimerisation domain	Domain
A, C, E	IPR028889	Ubiquitin specific protease UPS, catalytic domain	Domain
A, C, E	IPR001394	Peptidase C19, ubiquitin carboxyl-terminal hydrolase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F	Pharos: Q9H4P4	astrocytic tumor glioblastoma malignant glioma primitive neuroectodermal tumor subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor major depressive disorder osteosarcoma psoriasis Unipolar Depression bipolar disorder malignant ependymoma pilocytic astrocytoma skin disease
A, C, E	Pharos: P40818	Cushing disease due to pituitary adenoma ACTH-dependent Cushing syndrome acne DOID:12252 osteoarthritis tuberculosis Cushing syndrome hypertensive disorder ovarian cancer ankylosing spondylitis diabetes mellitus

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.