7ZJ3

Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate

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)
B [auth E]	SCOP2B Superfamily	UBC-like	8059970	3000570	SCOP2B (2022-06-29)
E [auth H]	SCOP2B Superfamily	UBC-like	8059970	3000570	SCOP2B (2022-06-29)
H [auth K]	SCOP2B Superfamily	UBC-like	8059970	3000570	SCOP2B (2022-06-29)
L [auth B]	SCOP2B Superfamily	UBC-like	8059970	3000570	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
F [auth I]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
I [auth L]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	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 [auth D]	PF13445	e7zj3D1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13445	ECOD (1.6)
G [auth J]	PF13445	e7zj3J1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13445	ECOD (1.6)
J [auth A]	PF13445	e7zj3A1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13445	ECOD (1.6)
D [auth G]	PF13445	e7zj3G1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: RING/U-box	F: PF13445	ECOD (1.6)
B [auth E]	PF00179	e7zj3E1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
E [auth H]	PF00179	e7zj3H1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
H [auth K]	PF00179	e7zj3K1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
L [auth B]	PF00179	e7zj3B1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: PF00179	ECOD (1.6)
C [auth F]	PF00240	e7zj3F1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
F [auth I]	PF00240	e7zj3I1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
I [auth L]	PF00240	e7zj3L1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
K [auth C]	PF00240	e7zj3C1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], D [auth G], G [auth J], J [auth A]	PF13445	RING-type zinc-finger (zf-RING_UBOX)	RING-type zinc-finger	This zinc-finger is a typical RING-type of plant ubiquitin ligases [1].	Domain
B [auth E], E [auth H], H [auth K], L [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
C [auth F], F [auth I], I [auth L], K [auth C]	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], D [auth G], G [auth J], J [auth A]	Tripartite motif-containing protein 2	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity translation regulator activity translation repressor activity cation binding transition metal ion binding zinc ion binding ion binding binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity translation regulator activity translation repressor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding ubiquitin-like protein ligase activity ubiquitin protein ligase activity	organonitrogen compound metabolic process protein polyubiquitination primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification metabolic 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 regulation of cellular process organonitrogen compound metabolic process protein polyubiquitination primary metabolic process organic substance metabolic process protein ubiquitination macromolecule modification metabolic 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 regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance biosynthetic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process cellular process regulation of metabolic process neuron apoptotic process regulation of apoptotic process regulation of programmed cell death cell death apoptotic process programmed cell death regulation of neuron apoptotic process 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	intracellular anatomical structure cytoplasm cellular anatomical entity
B [auth E], E [auth H], H [auth K], L [auth B]	Ubiquitin-conjugating enzyme E2 D1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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 ubiquitin-like protein ligase activity ubiquitin protein ligase activity	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic 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 cellular response to stimulus regulation of cellular process response to stimulus 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 cellular process TORC1 signaling regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process regulation of metabolic process negative regulation of cellular 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 organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway cellular response to endogenous stimulus BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus cell surface receptor signaling pathway regulation of BMP signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of protein polyubiquitination positive regulation of protein polyubiquitination proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	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 ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex
C [auth F], F [auth I], I [auth L], K [auth C]	Polyubiquitin-C	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process 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	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], D [auth G], G [auth J], J [auth A]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A [auth D], D [auth G], G [auth J], J [auth A]	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A [auth D], D [auth G], G [auth J], J [auth A]	IPR001258	NHL repeat	Repeat
A [auth D], D [auth G], G [auth J], J [auth A]	IPR000315	B-box-type zinc finger	Domain
A [auth D], D [auth G], G [auth J], J [auth A]	IPR027370	Zinc finger, RING-type, eukaryotic	Domain
A [auth D], D [auth G], G [auth J], J [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth D], D [auth G], G [auth J], J [auth A]	IPR017868	Filamin/ABP280 repeat-like	Repeat
A [auth D], D [auth G], G [auth J], J [auth A]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth D], D [auth G], G [auth J], J [auth A]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A [auth D], D [auth G], G [auth J], J [auth A]	IPR003649	B-box, C-terminal	Domain
A [auth D], D [auth G], G [auth J], J [auth A]	IPR001841	Zinc finger, RING-type	Domain
A [auth D], D [auth G], G [auth J], J [auth A]	IPR001298	Filamin/ABP280 repeat	Repeat
B [auth E], E [auth H], H [auth K], L [auth B]	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
B [auth E], E [auth H], H [auth K], L [auth B]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
B [auth E], E [auth H], H [auth K], L [auth B]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site
C [auth F], F [auth I], I [auth L], K [auth C]	IPR019954	Ubiquitin conserved site	Conserved Site
C [auth F], F [auth I], I [auth L], K [auth C]	IPR000626	Ubiquitin-like domain	Domain
C [auth F], F [auth I], I [auth L], K [auth C]	IPR019956	Ubiquitin domain	Domain
C [auth F], F [auth I], I [auth L], K [auth C]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D], D [auth G], G [auth J], J [auth A]	Pharos: Q9C040	Charcot-Marie-Tooth disease Charcot-Marie-Tooth disease type 2R peripheral neuropathy Osteoarthrosis Deformans pancreatic intraductal papillary-mucinous carcinoma peripheral nervous system disease pilocytic astrocytoma spina bifida atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant glioma motor peripheral neuropathy osteoarthritis osteosarcoma Charcot-Marie-Tooth disease Charcot-Marie-Tooth disease type 2R peripheral neuropathy Osteoarthrosis Deformans pancreatic intraductal papillary-mucinous carcinoma peripheral nervous system disease pilocytic astrocytoma spina bifida atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant glioma motor peripheral neuropathy osteoarthritis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm progressive supranuclear palsy ulcerative colitis breast cancer interstitial cystitis lung adenocarcinoma malignant mesothelioma neurodegenerative disease osteoarthritis susceptibility 1 ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Pick disease psoriasis breast carcinoma cystic fibrosis invasive ductal breast carcinoma lung carcinoma medulloblastoma non-small cell lung carcinoma
B [auth E], E [auth H], H [auth K], L [auth B]	Pharos: P51668	adenoma Duchenne muscular dystrophy malignant mesothelioma ovarian cancer Crohn disease inflammatory bowel disease medulloblastoma sarcoidosis cutaneous lupus erythematosus limb-girdle muscular dystrophy myopathy
C [auth F], F [auth I], I [auth L], K [auth C]	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm 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 R01GM133198.