8UQ8 | pdb_00008uq8

Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker

External Resource: Annotation

Domain Annotation: SCOP2 Classification
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)
B [auth a]	SCOP2B Superfamily	Core histone-like	8066283	3001387	SCOP2B (2022-06-29)
B [auth a]	SCOP2B Superfamily	Core histone-like	8039342	3001387	SCOP2B (2022-06-29)
B [auth a]	SCOP2B Superfamily	UBC-like	8033550	3000570	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8066283	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8039342	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UBC-like	8033550	3000570	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth a]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
A, B [auth a]	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain
A, B [auth a]	PF14447	Prokaryotic RING finger family 4 (Prok-RING_4)	Prokaryotic RING finger family 4	-	Family
A, B [auth a]	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth a]	E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin ubiquitin conjugating enzyme activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein conjugating enzyme activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding histone binding histone H2A ubiquitin ligase activity histone ubiquitin ligase activity histone H2AK15 ubiquitin ligase activity histone modifying activity chromatin binding ubiquitin binding ubiquitin-like protein binding polyubiquitin modification-dependent protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding cation binding transition metal ion binding zinc ion binding metal ion binding protein-containing complex binding nucleosome binding	negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process localization protein localization to chromatin protein localization to chromosome protein localization to chromosome, centromeric region protein localization to organelle macromolecule localization protein localization to CENP-A containing chromatin intracellular protein localization macromolecule modification primary metabolic process protein metabolic process protein modification process apoptotic process cell death programmed cell death protein autoubiquitination protein ubiquitination post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus signaling negative regulation of signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway negative regulation of cell communication cell communication cellular response to endogenous stimulus signal transduction BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of signaling cell surface receptor signaling pathway regulation of BMP signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction response to BMP regulation of response to stimulus regulation of cell communication transforming growth factor beta receptor superfamily signaling pathway response to growth factor negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process regulation of localization establishment of protein localization regulation of protein localization protein targeting regulation of protein targeting to mitochondrion regulation of establishment of protein localization positive regulation of biological process positive regulation of establishment of protein localization establishment of localization regulation of establishment of protein localization to mitochondrion establishment of protein localization to organelle regulation of protein targeting protein targeting to mitochondrion positive regulation of protein targeting to mitochondrion establishment of protein localization to mitochondrion positive regulation of establishment of protein localization to mitochondrion protein K6-linked ubiquitination protein polyubiquitination DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress DNA repair protein K11-linked ubiquitination protein K48-linked ubiquitination RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process protein monoubiquitination protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization protein-containing complex assembly nucleosome assembly nucleosome organization biological process involved in interspecies interaction between organisms innate immune response in mucosa immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus mucosal immune response organ or tissue specific immune response humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide antibacterial humoral response defense response to bacterium response to bacterium defense response to Gram-positive bacterium DNA repair-dependent chromatin remodeling double-strand break repair via classical nonhomologous end joining double-strand break repair double-strand break repair via nonhomologous end joining transcription elongation by RNA polymerase II negative regulation of transcription elongation by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II negative regulation of DNA-templated transcription, elongation DNA-templated transcription elongation interstrand cross-link repair regulation of cellular response to stress positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of DNA repair positive regulation of DNA metabolic process regulation of DNA metabolic process response to ionizing radiation response to radiation response to abiotic stimulus protein K63-linked ubiquitination immune system development adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process lymphocyte mediated immunity immunoglobulin production immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination B cell activation involved in immune response lymphocyte activation cell activation involved in immune response leukocyte activation multicellular organism development somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response anatomical structure development leukocyte mediated immunity somatic diversification of immune receptors lymphocyte activation involved in immune response somatic recombination of immunoglobulin genes involved in immune response system development developmental process production of molecular mediator of immune response B cell activation DNA recombination cell activation immunoglobulin mediated immune response adaptive immune response immune effector process somatic diversification of immunoglobulins somatic diversification of immune receptors via germline recombination within a single locus B cell mediated immunity isotype switching	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome membraneless organelle chromosome, centromeric region nucleus intracellular membrane-bounded organelle cytoplasm cytosol cell periphery plasma membrane membrane membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endosome membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane site of double-strand break site of DNA damage ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth a]	IPR009072	Histone-fold	Homologous Superfamily
A, B [auth a]	IPR002119	Histone H2A	Family
A, B [auth a]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, B [auth a]	IPR032454	Histone H2A, C-terminal domain	Domain
A, B [auth a]	IPR032458	Histone H2A conserved site	Conserved Site
A, B [auth a]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A, B [auth a]	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A, B [auth a]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
A, B [auth a]	IPR009072	Histone-fold	Homologous Superfamily
A, B [auth a]	IPR000558	Histone H2B	Family
A, B [auth a]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, B [auth a]	IPR055333	Histone H2B, conserved site	Conserved Site
A, B [auth a]	IPR051657	RNF168/RNF169 E3 ubiquitin-protein ligase	Family
A, B [auth a]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B [auth a]	IPR034725	E3 ubiquitin-protein ligase RNF168	Family
A, B [auth a]	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth a]	Pharos: Q8IYW5	juvenile idiopathic arthritis pituitary cancer acute myeloid leukemia autism spectrum disorder hypertensive disorder lung adenocarcinoma medulloblastoma ovarian cancer psoriasis allergic rhinitis breast cancer invasive ductal breast carcinoma Juvenile psoriatic arthritis lung cancer non-small cell lung carcinoma juvenile idiopathic arthritis pituitary cancer acute myeloid leukemia autism spectrum disorder hypertensive disorder lung adenocarcinoma medulloblastoma ovarian cancer psoriasis allergic rhinitis breast cancer invasive ductal breast carcinoma Juvenile psoriatic arthritis lung cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma squamous cell lung carcinoma atypical teratoid rhabdoid tumor ductal breast carcinoma in situ lung carcinoma osteoarthritis pancreatic intraductal papillary-mucinous neoplasm pituitary cancer rheumatoid arthritis astrocytic tumor autism spectrum disorder endogenous depression IgA glomerulonephritis malignant ependymoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell myeloma attention deficit hyperactivity disorder, inattentive type Down syndrome esophageal adenocarcinoma juvenile dermatomyositis medulloblastoma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma Pick disease progressive supranuclear palsy atypical teratoid rhabdoid tumor Emery-Dreifuss muscular dystrophy glioblastoma large cell medulloblastoma myopathy ovarian cancer breast carcinoma spina bifida breast cancer cystic fibrosis invasive ductal breast carcinoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma ductal breast carcinoma in situ lung carcinoma medulloblastoma ovarian cancer pilocytic astrocytoma psoriasis cancer idiopathic scoliosis malignant colon neoplasm nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer RIDDLE syndrome hereditary spastic paraplegia ovarian cancer intellectual disability osteosarcoma

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.