2N9P | pdb_00002n9p

Solution structure of RNF126 N-terminal zinc finger domain in complex with BAG6 Ubiquitin-like domain

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)
B [auth C]	d2n9pc1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d2n9pc2	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)
B [auth C]	SCOP2B Superfamily	Ubiquitin-like	8033367	3000157	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)
B [auth C]	ubiquitin_4	e2n9pC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_4	ECOD (1.6)
A	zinc_ribbon_9	e2n9pA1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zinc_ribbon_9	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	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
A	PF14369	zinc-ribbon (Zn_ribbon_19)	zinc-ribbon		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	Large proline-rich protein BAG6	protein binding binding misfolded protein binding protein carrier chaperone molecular carrier activity ubiquitin-specific protease binding enzyme binding protease binding polyubiquitin modification-dependent protein binding modification-dependent protein binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein-containing complex binding protein binding binding misfolded protein binding protein carrier chaperone molecular carrier activity ubiquitin-specific protease binding enzyme binding protease binding polyubiquitin modification-dependent protein binding modification-dependent protein binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein-containing complex binding proteasome binding identical protein binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity Hsp70 protein binding protein-folding chaperone binding heat shock protein binding ribonucleoprotein complex binding ribosome binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of protein stability biological regulation regulation of biological quality protein stabilization cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress meiotic chromosome segregation synaptonemal complex assembly meiotic cell cycle process cellular component organization cellular component biogenesis cellular component assembly meiosis I meiotic nuclear division cellular component organization or biogenesis cell cycle synaptonemal complex organization chromosome segregation cell cycle process meiotic cell cycle organelle fission chromosome organization chromosome organization involved in meiotic cell cycle organelle organization nuclear division meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation membrane organization establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane tail-anchored membrane protein insertion into ER membrane endoplasmic reticulum organization establishment of localization localization protein localization to organelle macromolecule localization intracellular protein localization protein insertion into membrane protein insertion into ER membrane endomembrane system organization apoptotic process cell death programmed cell death regulation of cellular process negative regulation of proteolysis negative regulation of proteolysis involved in protein catabolic process negative regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process negative regulation of protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process regulation of biological process negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process regulation of metabolic process regulation of protein catabolic process immune response-regulating cell surface receptor signaling pathway signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response regulation of response to stimulus immune system process regulation of immune response activation of immune response cell activation natural killer cell activation lymphocyte activation leukocyte activation maintenance of unfolded protein kidney development renal system development chromatin organization cellular developmental process cell differentiation T cell activation alpha-beta T cell activation NK T cell activation negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process tube development respiratory tube development lung development respiratory system development protein targeting post-translational protein targeting to endoplasmic reticulum membrane protein targeting to membrane establishment of protein localization to organelle establishment of protein localization to endoplasmic reticulum protein targeting to ER endoplasmic reticulum stress-induced pre-emptive quality control intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress intracellular signal transduction apoptotic signaling pathway intrinsic apoptotic signaling pathway signal transduction by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator DNA damage response intrinsic apoptotic signaling pathway by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development regulation of multicellular organismal process peptidyl-lysine acetylation peptidyl-lysine modification protein acylation protein acetylation internal peptidyl-lysine acetylation macromolecule modification peptidyl-amino acid modification protein modification process internal protein amino acid acetylation positive regulation of proteasomal protein catabolic process regulation of cellular response to stress positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of ERAD pathway positive regulation of protein catabolic process positive regulation of proteolysis positive regulation of ERAD pathway positive regulation of protein metabolic process regulation of response to endoplasmic reticulum stress positive regulation of response to endoplasmic reticulum stress regulation of response to stress positive regulation of cellular process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex BAT3 complex ER membrane insertion complex
A	E3 ubiquitin-protein ligase RNF126	epidermal growth factor receptor binding protein binding binding signaling receptor binding growth factor receptor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein epidermal growth factor receptor binding protein binding binding signaling receptor binding growth factor receptor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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	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 ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus 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 ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress recombinational repair positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination positive regulation of cellular process DNA repair positive regulation of DNA recombination double-strand break repair regulation of biological process DNA recombination biological regulation DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair regulation of double-strand break repair via homologous recombination positive regulation of DNA metabolic process DNA damage response regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process protein polyubiquitination protein K63-linked ubiquitination 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 protein K27-linked ubiquitination protein K48-linked ubiquitination cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cytoplasm protein quality control proteasome-mediated ubiquitin-dependent protein catabolic process cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein cytoplasm protein quality control by the ubiquitin-proteasome system proteasomal protein catabolic process response to topologically incorrect protein protein quality control for misfolded or incompletely synthesized proteins cell population proliferation regulation of cell population proliferation protein K29-linked ubiquitination ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway signaling negative regulation of signaling negative regulation of ERBB signaling pathway negative regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication regulation of epidermal growth factor receptor signaling pathway negative regulation of cellular process epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway regulation of cell communication protein monoubiquitination	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR019954	Ubiquitin conserved site	Conserved Site
B [auth C]	IPR000626	Ubiquitin-like domain	Domain
B [auth C]	IPR048926	Bag6, BAG-similar domain	Domain
B [auth C]	IPR021925	Large proline-rich protein BAG6	Domain
B [auth C]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR039525	E3 ubiquitin-protein ligase RNF126-like, zinc-ribbon	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C]	Pharos: P46379	rheumatoid arthritis astrocytic tumor Crohn disease hypertensive disorder lung carcinoma membranous glomerulonephritis ovarian cancer squamous cell lung carcinoma autism spectrum disorder cutaneous lupus erythematosus laryngeal squamous cell carcinoma malignant mesothelioma myositis psoriatic arthritis systemic lupus erythematosus rheumatoid arthritis astrocytic tumor Crohn disease hypertensive disorder lung carcinoma membranous glomerulonephritis ovarian cancer squamous cell lung carcinoma autism spectrum disorder cutaneous lupus erythematosus laryngeal squamous cell carcinoma malignant mesothelioma myositis psoriatic arthritis systemic lupus erythematosus cancer Hashimoto thyroiditis lung adenocarcinoma medulloblastoma osteosarcoma
A	Pharos: Q9BV68	ovarian cancer Sjogren syndrome psoriasis rheumatoid arthritis

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.