8A58

X-ray structure of TRIM21 RING E3 ligase in complex with E2 enzyme Ube2W

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)
A	SCOP2B Superfamily	UBC-like	8036719	3000570	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	UBC-like	8036719	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	F_UNCLASSIFIED	e8a58A1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth B]	F_UNCLASSIFIED	e8a58B1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth C]	F_UNCLASSIFIED	e8a58C1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth D]	F_UNCLASSIFIED	e8a58D1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
D [auth B]	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	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 [auth C], C [auth D]	PF00097	Zinc finger, C3HC4 type (RING finger) (zf-C3HC4)	Zinc finger, C3HC4 type (RING finger)	The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many protein ...	The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid [1]. Many proteins containing a RING finger play a key role in the ubiquitination pathway [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth B]	Ubiquitin-conjugating enzyme E2 W	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 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 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 protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding	protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal biological process involved in interspecies interaction between organisms response to stimulus protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus immune system process defense response to other organism response to stress innate immune response antiviral innate immune response response to external biotic stimulus response to virus cellular response to stimulus DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response DNA repair protein K11-linked ubiquitination regulation of cellular process signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication negative regulation of TORC1 signaling regulation of intracellular signal transduction negative regulation of TOR signaling negative regulation of cellular process signal transduction regulation of TORC1 signaling TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling negative regulation of response to stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus regulation of cell communication TORC1 signaling cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein response to topologically incorrect protein protein monoubiquitination catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process proteolysis protein quality control for misfolded or incompletely synthesized proteins proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B [auth C], C [auth D]	E3 ubiquitin-protein ligase TRIM21	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 DNA binding binding nucleic acid binding identical protein binding 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 DNA binding binding nucleic acid binding identical protein binding protein binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding protein homodimerization activity protein dimerization activity kinase binding enzyme binding protein kinase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	protein destabilization regulation of protein stability biological regulation regulation of biological quality protein polyubiquitination primary metabolic process protein K27-linked ubiquitination protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein destabilization regulation of protein stability biological regulation regulation of biological quality protein polyubiquitination primary metabolic process protein K27-linked ubiquitination protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process protein catabolic process macromolecule catabolic process proteolysis regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of DNA-binding transcription factor activity regulation of DNA-templated transcription biological process involved in interspecies interaction between organisms response to stimulus 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 response to stress innate immune response response to external biotic stimulus protein autoubiquitination protein K6-linked ubiquitination response to type II interferon response to cytokine response to peptide response to chemical protein K48-linked ubiquitination positive regulation of viral life cycle positive regulation of viral process positive regulation of biological process viral life cycle modulation by symbiont of entry into host biological process involved in interaction with host biological process involved in symbiotic interaction regulation of viral entry into host cell regulation of viral life cycle regulation of viral process symbiont entry into host cell viral process symbiont entry into host positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction protein monoubiquitination positive regulation of autophagy autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process process utilizing autophagic mechanism positive regulation of cellular process regulation of protein binding positive regulation of protein binding regulation of binding positive regulation of binding cell cycle regulation of cell cycle positive regulation of cell cycle cellular response to stimulus 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 positive regulation of response to stimulus 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 response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling cellular component disassembly protein-containing complex organization protein-containing complex disassembly protein-RNA complex disassembly cellular component organization organelle organization protein-RNA complex organization organelle disassembly cellular component organization or biogenesis stress granule disassembly multicellular organismal process type I interferon production cytokine production regulation of cytokine production regulation of multicellular organismal process regulation of type I interferon production regulation of defense response regulation of response to biotic stimulus negative regulation of response to biotic stimulus regulation of response to external stimulus negative regulation of biological process regulation of response to stress regulation of immune system process negative regulation of response to stimulus regulation of innate immune response negative regulation of immune response negative regulation of immune system process negative regulation of response to external stimulus negative regulation of defense response regulation of immune response negative regulation of innate immune response defense response to virus suppression of viral release by host response to virus negative regulation of DNA-binding transcription factor activity negative regulation of NF-kappaB transcription factor activity negative regulation of molecular function protein K63-linked ubiquitination protein localization regulation of localization cellular localization regulation of protein localization localization regulation of cellular localization cellular macromolecule localization macromolecule localization viral gene expression negative regulation of viral process regulation of viral transcription negative regulation of viral transcription viral transcription cellular response to chemical stimulus cellular response to stress cellular response to chemical stress negative regulation of post-translational protein modification protein deubiquitination regulation of protein modification process protein modification by small protein removal negative regulation of protein modification process negative regulation of cellular process regulation of protein modification by small protein conjugation or removal negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process negative regulation of protein deubiquitination regulation of protein deubiquitination pyroptotic inflammatory response inflammatory response	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle vacuole autophagosome intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle vacuole autophagosome intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cytoplasmic vesicle intracellular vesicle vesicle P-body protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR050113	Ubiquitin-conjugating enzyme	Family
A, D [auth B]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A, D [auth B]	IPR000608	Ubiquitin-conjugating enzyme E2, catalytic core domain	Domain
B [auth C], C [auth D]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
B [auth C], C [auth D]	IPR003877	SPRY domain	Domain
B [auth C], C [auth D]	IPR003613	U-box domain	Domain
B [auth C], C [auth D]	IPR001870	B30.2/SPRY domain	Domain
B [auth C], C [auth D]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B [auth C], C [auth D]	IPR003879	Butyrophylin-like, SPRY domain	Domain
B [auth C], C [auth D]	IPR050143	Tripartite motif-containing	Family
B [auth C], C [auth D]	IPR020457	Zinc finger, B-box, chordata	Domain
B [auth C], C [auth D]	IPR035831	TRIM21, PRY/SPRY domain	Domain
B [auth C], C [auth D]	IPR001841	Zinc finger, RING-type	Domain
B [auth C], C [auth D]	IPR006574	SPRY-associated	Domain
B [auth C], C [auth D]	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
B [auth C], C [auth D]	IPR018957	Zinc finger, C3HC4 RING-type	Domain
B [auth C], C [auth D]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
B [auth C], C [auth D]	IPR000315	B-box-type zinc finger	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D [auth B]	Pharos: Q96B02	astrocytic tumor glioblastoma large cell medulloblastoma myopathy ovarian cancer atypical teratoid rhabdoid tumor invasive ductal breast carcinoma malignant glioma oligodendroglioma primitive neuroectodermal tumor breast cancer juvenile dermatomyositis medulloblastoma osteosarcoma rheumatoid arthritis
B [auth C], C [auth D]	Pharos: P19474	atrioventricular block glioblastoma lung carcinoma osteosarcoma autoimmune disease juvenile dermatomyositis multiple sclerosis pilocytic astrocytoma cutaneous lupus erythematosus lung cancer myositis Potocki-Shaffer syndrome

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.