3LRQ | pdb_00003lrq

Crystal structure of the U-box domain of human ubiquitin-protein ligase (E3), NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR4604D.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d3lrqd_	Small proteins	RING/U-box	RING/U-box	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3lrqc_	Small proteins	RING/U-box	RING/U-box	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3lrqb1	Small proteins	RING/U-box	RING/U-box	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3lrqb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3lrqa1	Small proteins	RING/U-box	RING/U-box	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3lrqa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	RVP	e3lrqD1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
C	RVP	e3lrqC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
B	RVP	e3lrqB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
A	Pyrophosphatase	e3lrqA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: sensor domains	T: sensor domains	F: Pyrophosphatase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	E3 ubiquitin-protein ligase TRIM37	chromatin binding binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity histone H2A ubiquitin ligase activity catalytic activity, acting on a protein acyltransferase activity histone H2AK119 ubiquitin ligase activity transferase activity histone ubiquitin ligase activity chromatin binding binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity histone H2A ubiquitin ligase activity catalytic activity, acting on a protein acyltransferase activity histone H2AK119 ubiquitin ligase activity transferase activity histone ubiquitin ligase activity ubiquitin-protein transferase activity ubiquitin-like protein transferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity histone modifying activity catalytic activity identical protein binding 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 signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding	regulation of protein stability biological regulation regulation of biological quality protein stabilization protein autoubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process regulation of protein stability biological regulation regulation of biological quality protein stabilization protein autoubiquitination 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 cellular localization establishment of protein localization protein localization to peroxisome protein transmembrane import into intracellular organelle transport peroxisomal membrane transport cellular component organization localization peroxisome organization protein transmembrane transport establishment of localization in cell cellular component organization or biogenesis intracellular protein localization establishment of protein localization to peroxisome intracellular protein transmembrane transport intracellular transport protein import into peroxisome matrix establishment of localization peroxisomal transport transmembrane transport organelle organization establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization intracellular protein transport regulation of cytoskeleton organization negative regulation of centriole replication regulation of cellular process regulation of cellular component organization microtubule cytoskeleton organization negative regulation of biological process membraneless organelle assembly negative regulation of cell cycle negative regulation of organelle assembly cellular component biogenesis centrosome duplication negative regulation of centrosome cycle cellular component assembly centrosome cycle negative regulation of cellular process cell cycle negative regulation of centrosome duplication regulation of cell cycle regulation of centriole replication centriole replication cell cycle process centriole assembly regulation of biological process microtubule organizing center organization organelle assembly negative regulation of cellular component organization regulation of cell cycle process negative regulation of cytoskeleton organization regulation of centrosome cycle regulation of microtubule-based process negative regulation of cell cycle process regulation of cellular component biogenesis regulation of organelle organization negative regulation of organelle organization regulation of centrosome duplication regulation of organelle assembly microtubule-based process cytoskeleton organization chromatin organization chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process epigenetic regulation of gene expression negative regulation of metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process aggresome assembly inclusion body assembly RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process 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 RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of RNA metabolic process protein monoubiquitination	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex histone methyltransferase complex catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex histone methyltransferase complex catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen PcG protein complex intracellular organelle nucleoplasm organelle lumen organelle methyltransferase complex ESC/E(Z) complex nuclear lumen inclusion body aggresome membraneless organelle intracellular membraneless organelle chromosome peroxisome microbody perinuclear region of cytoplasm membrane microbody membrane bounding membrane of organelle peroxisomal membrane organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002083	MATH/TRAF domain	Domain
A, B, C, D	IPR000315	B-box-type zinc finger	Domain
A, B, C, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D	IPR053003	TRIM/RBCC E3 ubiquitin-protein ligases	Family
A, B, C, D	IPR037299	TRIM37, MATH domain	Domain
A, B, C, D	IPR003649	B-box, C-terminal	Domain
A, B, C, D	IPR001841	Zinc finger, RING-type	Domain
A, B, C, D	IPR008974	TRAF-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O94972	mulibrey nanism Craniofacial Abnormalities McCune-Albright syndrome peroxisomal disease plasma cell myeloma astrocytic tumor IgA glomerulonephritis large cell medulloblastoma malignant glioma osteitis fibrosa osteosarcoma Pick disease subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma mulibrey nanism Craniofacial Abnormalities McCune-Albright syndrome peroxisomal disease plasma cell myeloma astrocytic tumor IgA glomerulonephritis large cell medulloblastoma malignant glioma osteitis fibrosa osteosarcoma Pick disease subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor glioblastoma intellectual disability lung cancer ovarian cancer pilocytic astrocytoma cancer invasive ductal breast carcinoma malignant ependymoma osteogenesis imperfecta

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.