8UQB

Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1)

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)
A	SCOP2B Superfamily	Core histone-like	8066283	3001387	SCOP2B (2021-05-27)
A	SCOP2B Superfamily	UBC-like	8033550	3000570	SCOP2B (2021-05-27)
A	SCOP2B Superfamily	Core histone-like	8039342	3001387	SCOP2B (2021-05-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
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	PF14447	Prokaryotic RING finger family 4 (Prok-RING_4)	Prokaryotic RING finger family 4	-	Family
A	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR034725	E3 ubiquitin-protein ligase RNF168	Family
A	IPR001841	Zinc finger, RING-type	Domain
A	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
A	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
A	IPR009072	Histone-fold	Homologous Superfamily
A	IPR007125	Histone H2A/H2B/H3	Domain
A	IPR000558	Histone H2B	Family
A	IPR009072	Histone-fold	Homologous Superfamily
A	IPR007125	Histone H2A/H2B/H3	Domain
A	IPR002119	Histone H2A	Family
A	IPR032454	Histone H2A, C-terminal domain	Domain
A	IPR032458	Histone H2A conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P04908	RIDDLE syndrome hereditary spastic paraplegia ovarian cancer intellectual disability osteosarcoma 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 RIDDLE syndrome hereditary spastic paraplegia ovarian cancer intellectual disability osteosarcoma 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 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

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 R01GM133198.