4ORH

Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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	UBC-like	8034189	3000570	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	UBC-like	8034189	3000570	SCOP2B (2022-06-29)
H [auth I]	SCOP2B Superfamily	UBC-like	8034189	3000570	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	UBC-like	8034195	3000570	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	UBC-like	8034195	3000570	SCOP2B (2022-06-29)
I [auth J]	SCOP2B Superfamily	UBC-like	8034195	3000570	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	PF00179	e4orhA1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
D [auth E]	PF00179	e4orhE1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
H [auth I]	PF00179	e4orhI1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
B	PF00179	e4orhB1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
E [auth F]	PF00179	e4orhF1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
I [auth J]	PF00179	e4orhJ1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
C	PF13920	e4orhC1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13920	ECOD (1.6)
F [auth G]	PF13920	e4orhG1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13920	ECOD (1.6)
G [auth H]	PF13920	e4orhH1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13920	ECOD (1.6)
J [auth K]	PF13920	e4orhK1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13920	ECOD (1.6)
K [auth L]	PF13920	e4orhL1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13920	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth E], H [auth I]	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
B, E [auth F], I [auth J]	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
C, F [auth G], G [auth H], J [auth K], K [auth L]	PF13920	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_3)	Zinc finger, C3HC4 type (RING finger)	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth E], H [auth I]	Ubiquitin-conjugating enzyme E2 variant 2	-	cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair organic substance metabolic process cellular response to stress response to stress regulation of response to stress cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair organic substance metabolic process cellular response to stress response to stress regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process DNA repair double-strand break repair regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process positive regulation of double-strand break repair nucleic acid metabolic process regulation of DNA repair organic cyclic compound metabolic process positive regulation of DNA metabolic process regulation of response to stimulus DNA damage response metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process organonitrogen compound metabolic process protein polyubiquitination 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 DNA double-strand break processing protein K63-linked ubiquitination regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of protein K63-linked ubiquitination positive regulation of protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of protein K63-linked ubiquitination positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of protein polyubiquitination regulation of post-translational protein modification regulation of protein metabolic process positive regulation of protein polyubiquitination postreplication repair error-free postreplication DNA repair	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle ubiquitin conjugating enzyme complex protein-containing complex catalytic complex UBC13-MMS2 complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle ubiquitin conjugating enzyme complex protein-containing complex catalytic complex UBC13-MMS2 complex transferase complex intracellular protein-containing complex intracellular anatomical structure cytoplasm nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen
B, E [auth F], I [auth J]	Ubiquitin-conjugating enzyme E2 N	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 enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity 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 enzyme regulator activity enzyme activator activity ubiquitin-protein transferase regulator activity molecular function activator activity molecular function regulator activity ubiquitin-protein transferase activator activity protein binding binding ubiquitin binding ubiquitin-like protein binding RNA binding organic cyclic compound binding nucleic acid binding 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 ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair organic substance metabolic process cellular response to stress response to stress regulation of response to stress cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair organic substance metabolic process cellular response to stress response to stress regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process DNA repair double-strand break repair regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process positive regulation of double-strand break repair nucleic acid metabolic process regulation of DNA repair organic cyclic compound metabolic process positive regulation of DNA metabolic process regulation of response to stimulus DNA damage response metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA double-strand break processing positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response 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 organonitrogen compound catabolic process 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 organic substance catabolic process postreplication repair positive regulation of DNA-binding transcription factor activity cellular biosynthetic process positive regulation of NF-kappaB transcription factor activity RNA metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription protein polyubiquitination protein K63-linked ubiquitination biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism innate immune response antiviral innate immune response response to external biotic stimulus response to virus DNA recombination recombinational repair double-strand break repair via homologous recombination negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of cell communication negative regulation of TORC1 signaling negative regulation of TOR signaling negative regulation of cellular process regulation of TORC1 signaling TOR signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction TORC1 signaling regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of protein K63-linked ubiquitination positive regulation of protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of protein K63-linked ubiquitination positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of protein polyubiquitination regulation of post-translational protein modification regulation of protein metabolic process positive regulation of protein polyubiquitination	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen protein-containing complex ubiquitin conjugating enzyme complex catalytic complex UBC13-UEV1A complex transferase complex intracellular protein-containing complex UBC13-MMS2 complex ubiquitin ligase complex
C, F [auth G], G [auth H], J [auth K], K [auth L]	E3 ubiquitin-protein ligase RNF8	protein binding binding histone binding protein-containing complex binding chromatin binding ubiquitin binding ubiquitin-like protein 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 protein binding binding histone binding protein-containing complex binding chromatin binding ubiquitin binding ubiquitin-like protein 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 identical protein binding protein homodimerization activity protein dimerization activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication signal transduction in response to DNA damage signal transduction cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication signal transduction in response to DNA damage signal transduction cell division 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 cellular biosynthetic process organic substance metabolic process organic substance biosynthetic process regulation of biosynthetic process epigenetic regulation of gene expression cellular metabolic process 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 metabolic process macromolecule metabolic 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 nucleobase-containing compound metabolic 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 primary metabolic process negative regulation of cellular biosynthetic process negative regulation of DNA-templated transcription, elongation organic cyclic compound metabolic process negative regulation of macromolecule biosynthetic process organic cyclic compound 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 nucleic acid metabolic process DNA-templated transcription elongation negative regulation of biosynthetic process organonitrogen compound metabolic process protein autoubiquitination 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 DNA metabolic process interstrand cross-link repair DNA repair 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 cell cycle 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 organic substance catabolic process response to ionizing radiation response to radiation response to abiotic stimulus spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation cell differentiation anatomical structure development sperm DNA condensation developmental process multicellular organismal reproductive process male gamete generation nucleus organization organelle organization germ cell development spermatid nucleus differentiation protein polyubiquitination protein K63-linked ubiquitination protein K48-linked ubiquitination double-strand break repair 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 leukocyte mediated immunity somatic diversification of immune receptors somatic recombination of immunoglobulin genes involved in immune response system development 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 double-strand break repair via nonhomologous end joining	midbody cellular anatomical entity 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 midbody cellular anatomical entity 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 site of double-strand break intracellular non-membrane-bounded organelle site of DNA damage chromosome non-membrane-bounded organelle chromosome, telomeric region chromosomal region protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth E], H [auth I]	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
A, D [auth E], H [auth I]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B, E [auth F], I [auth J]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B, E [auth F], I [auth J]	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
B, E [auth F], I [auth J]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
C, F [auth G], G [auth H], J [auth K], K [auth L]	IPR017335	E3 ubiquitin-protein ligase RNF8	Family
C, F [auth G], G [auth H], J [auth K], K [auth L]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
C, F [auth G], G [auth H], J [auth K], K [auth L]	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
C, F [auth G], G [auth H], J [auth K], K [auth L]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C, F [auth G], G [auth H], J [auth K], K [auth L]	IPR000253	Forkhead-associated (FHA) domain	Domain
C, F [auth G], G [auth H], J [auth K], K [auth L]	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D [auth E], H [auth I]	Pharos: Q15819	astrocytic tumor malignant ependymoma ovarian cancer atypical teratoid rhabdoid tumor malignant glioma Pick disease glioblastoma oligodendroglioma
B, E [auth F], I [auth J]	Pharos: P61088	Embryo Loss astrocytic tumor lymphoplasmacytic lymphoma osteosarcoma pituitary cancer invasive ductal breast carcinoma malignant ependymoma ovarian cancer psoriasis lung cancer oligodendroglioma Pick disease subependymal giant cell astrocytoma
C, F [auth G], G [auth H], J [auth K], K [auth L]	Pharos: O76064	autism Autistic Disorder RIDDLE syndrome

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.