2MJ5

Structure of the UBA Domain of Human NBR1 in Complex with Ubiquitin

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)
A	d2mj5a_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2mj5b1	All alpha proteins	RuvA C-terminal domain-like	UBA-like	UBA domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2mj5b2	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)
A	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	UBA-like	8039181	3001235	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	ubiquitin_1	e2mj5A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	UNK_F_TYPE	e2mj5B1	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	Polyubiquitin-C	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding RNA binding organic cyclic compound binding nucleic acid binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process protein ubiquitination macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process 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	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B	Next to BRCA1 gene 1 protein	protein binding binding ubiquitin binding ubiquitin-like protein binding kinase binding enzyme binding protein kinase binding mitogen-activated protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	developmental process regulation of osteoblast differentiation multicellular organismal process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of osteoblast differentiation negative regulation of developmental process biological regulation negative regulation of biological process regulation of cell differentiation osteoblast differentiation ossification cell differentiation developmental process regulation of osteoblast differentiation multicellular organismal process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of osteoblast differentiation negative regulation of developmental process biological regulation negative regulation of biological process regulation of cell differentiation osteoblast differentiation ossification cell differentiation negative regulation of cellular process negative regulation of cell differentiation cellular process cellular response to stimulus response to stimulus signaling regulation of cellular response to stress regulation of signal transduction intracellular signal transduction cell communication stress-activated MAPK cascade cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress intracellular signaling cassette signal transduction regulation of signaling regulation of stress-activated protein kinase signaling cascade regulation of MAPK cascade regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade regulation of response to stimulus MAPK cascade regulation of cell communication regulation of multicellular organismal development bone mineralization animal organ development regulation of biomineral tissue development regulation of bone mineralization tissue development multicellular organism development anatomical structure development biomineral tissue development regulation of multicellular organismal process regulation of ossification catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism	M band intracellular anatomical structure intracellular membraneless organelle sarcomere intracellular organelle cellular anatomical structure organelle membraneless organelle contractile muscle fiber A band cytoplasm supramolecular fiber myofibril supramolecular polymer M band intracellular anatomical structure intracellular membraneless organelle sarcomere intracellular organelle cellular anatomical structure organelle membraneless organelle contractile muscle fiber A band cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex membrane cytosol membrane-bounded organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen lytic vacuole vacuole lysosome protein-containing complex receptor complex autophagosome peroxisome microbody membrane bounding membrane of organelle peroxisomal membrane microbody organelle membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle late endosome vesicle nuclear body mitochondrial intermembrane space mitochondrion organelle envelope lumen organelle envelope mitochondrial envelope phagophore assembly site

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR019954	Ubiquitin conserved site	Conserved Site
A	IPR000626	Ubiquitin-like domain	Domain
A	IPR019956	Ubiquitin domain	Domain
A	IPR050158	Ubiquitin and ubiquitin-like	Family
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR043145	Zinc finger, ZZ-type superfamily	Homologous Superfamily
B	IPR032350	Next to BRCA1, central domain	Domain
B	IPR000270	PB1 domain	Domain
B	IPR000433	Zinc finger, ZZ-type	Domain
B	IPR015940	Ubiquitin-associated domain	Domain
B	IPR034852	NBR1, PB1 domain	Domain
B	IPR053793	PB1-like domain	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR009060	UBA-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer
B	Pharos: Q14596	astrocytic tumor Gaucher disease malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Sjogren syndrome dermatomyositis interstitial lung disease medulloblastoma ovarian cancer Pick disease subependymal giant cell astrocytoma diabetes mellitus lymphoplasmacytic lymphoma oligodendroglioma astrocytic tumor Gaucher disease malignant ependymoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Sjogren syndrome dermatomyositis interstitial lung disease medulloblastoma ovarian cancer Pick disease subependymal giant cell astrocytoma diabetes mellitus lymphoplasmacytic lymphoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma

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.