4OLE | pdb_00004ole

Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution

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)
C	SCOP2B Superfamily	E set domains	8054003	3000070	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	E set domains	8054003	3000070	SCOP2B (2022-06-29)
B	SCOP2 Family	NBR1 domain-like	8044994	4004242	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	E set domains	8054003	3000070	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	E set domains	8054003	3000070	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)
C	DUF4170	e4oleC1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: DUF4170	ECOD (v294.1)
D	DUF4170	e4oleD1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: DUF4170	ECOD (v294.1)
B	Rep-A_N	e4oleB1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Rep-A_N	ECOD (v294.1)
A	QRPTase_N	e4oleA1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Nicotinate/Quinolinate PRTase N-terminal domain-like	F: QRPTase_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF16158	Ig-like domain from next to BRCA1 gene (N_BRCA1_IG)	Ig-like domain from next to BRCA1 gene	Domain present between positions 365-485 in the human next to BRCA1 gene 1 protein Q14596 (NBR1_HUMAN) Distant homology and fold prediction analysis suggests this domain has an immunoglobulin like fold and is distantly homologous to domains involved ...	Domain present between positions 365-485 in the human next to BRCA1 gene 1 protein Q14596 (NBR1_HUMAN) Distant homology and fold prediction analysis suggests this domain has an immunoglobulin like fold and is distantly homologous to domains involved in cell adhesion such as CARDB (PF07705). JCSG construct was crystalized confirming the domain boundaries	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	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 nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen lytic vacuole vacuole lysosome protein-containing complex signaling 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, B, C, D	IPR043145	Zinc finger, ZZ-type superfamily	Homologous Superfamily
A, B, C, D	IPR034852	Nbr1, PB1 domain	Domain
A, B, C, D	IPR056893	Nbr1-like, C-terminal UBA domain	Domain
A, B, C, D	IPR000270	PB1 domain	Domain
A, B, C, D	IPR000433	Zinc finger, ZZ-type	Domain
A, B, C, D	IPR015940	Ubiquitin-associated domain	Domain
A, B, C, D	IPR032350	Nbr1, FW domain	Domain
A, B, C, D	IPR053793	PB1-like domain	Domain
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR009060	UBA-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.