6FGA

Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1

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)
I	d6fgai_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d6fgaj_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d6fgak_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
L	d6fgal_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M	d6fgam_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
N	d6fgan_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
O	d6fgao_	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	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)
I	SCOP2B Superfamily	UBC-like	8059968	3000570	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	UBC-like	8059968	3000570	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	UBC-like	8059968	3000570	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	UBC-like	8059968	3000570	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	UBC-like	8059968	3000570	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	UBC-like	8059968	3000570	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	UBC-like	8059968	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	zf-C3HC4_4	e6fgaA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_4	ECOD (1.6)
B	zf-C3HC4_4	e6fgaB1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_4	ECOD (1.6)
C	zf-C3HC4_4	e6fgaC1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_4	ECOD (1.6)
D	zf-C3HC4_4	e6fgaD1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_4	ECOD (1.6)
E	zf-C3HC4_4	e6fgaE1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_4	ECOD (1.6)
F	zf-C3HC4_4	e6fgaF1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_4	ECOD (1.6)
G	zf-C3HC4_4	e6fgaG1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_4	ECOD (1.6)
H	zf-C3HC4_4	e6fgaH1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: zf-C3HC4_4	ECOD (1.6)
I	UQ_con	e6fgaI1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
J	UQ_con	e6fgaJ1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
K	UQ_con	e6fgaK1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
L	UQ_con	e6fgaL1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
M	UQ_con	e6fgaM1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
N	UQ_con	e6fgaN1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
O	UQ_con	e6fgaO1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
D	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
E	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
F	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
G	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
H	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)
I	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
J	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
K	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
L	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
M	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
N	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
O	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, B, C, D, E A, B, C, D, E, F, G, H	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
I, J, K, L, M I, J, K, L, M, N, O	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	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
I, J, K, L, M I, J, K, L, M, N, O	Ubiquitin-conjugating enzyme E2 E1	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 ISG15 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 protein polyubiquitination 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 protein polyubiquitination 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 K48-linked ubiquitination ISG15-protein conjugation protein monoubiquitination regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	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 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 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, B, C, D, E A, B, C, D, E, F, G, H	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003877	SPRY domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003613	U-box domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001870	B30.2/SPRY domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003879	Butyrophylin-like, SPRY domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050143	Tripartite motif-containing	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020457	Zinc finger, B-box, chordata	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR035831	TRIM21, PRY/SPRY domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001841	Zinc finger, RING-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006574	SPRY-associated	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000315	B-box-type zinc finger	Domain
I, J, K, L, M I, J, K, L, M, N, O	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
I, J, K, L, M I, J, K, L, M, N, O	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
I, J, K, L, M I, J, K, L, M, N, O	IPR000608	Ubiquitin-conjugating enzyme E2, catalytic core domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	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
I, J, K, L, M I, J, K, L, M, N, O	Pharos: P51965	Arsenic Poisoning juvenile idiopathic arthritis amyotrophic lateral sclerosis myopathy plasma cell myeloma skin disease attention deficit hyperactivity disorder, inattentive type lung cancer ovarian cancer

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.