6XQI | pdb_00006xqi

Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A

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)
F [auth G]	SCOP2B Superfamily	UBA-like	8037710	3001235	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	UBA-like	8037710	3001235	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)
F [auth G]	Trypsin	e6xqiG1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin	ECOD (v294.1)
E [auth F]	RNase_H	e6xqiF1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: RNase_H	ECOD (v294.1)
D	Glyco_transf_41	e6xqiD1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (v294.1)
C	Glyco_transf_41	e6xqiC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (v294.1)
B	Glyco_transf_41	e6xqiB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (v294.1)
A	Glyco_transf_41	e6xqiA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth F], F [auth G]	PF00627	UBA/TS-N domain (UBA)	UBA/TS-N domain	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin a ...	This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle [1]. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU [2]. The domain has been found in non EF-TS proteins such as alpha-NAC Swiss:P70670 and MJ0280 Swiss:Q57728 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth H], H [auth I]	ASN-PRO-LEU-GLU-PHE-LEU	-	-	-
E [auth F], F [auth G]	UV excision repair protein RAD23 homolog A	protein binding binding ubiquitin binding ubiquitin-like protein binding DNA binding damaged DNA binding nucleic acid binding ubiquitin-specific protease binding enzyme binding protease binding kinase binding histone H4 demethylase activity catalytic activity, acting on a protein protein demethylase activity protein binding binding ubiquitin binding ubiquitin-like protein binding DNA binding damaged DNA binding nucleic acid binding ubiquitin-specific protease binding enzyme binding protease binding kinase binding histone H4 demethylase activity catalytic activity, acting on a protein protein demethylase activity histone H4K20 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone modifying activity 2-oxoglutarate-dependent dioxygenase activity catalytic activity polyubiquitin modification-dependent protein binding modification-dependent protein binding protein-containing complex binding proteasome binding single-stranded DNA binding	regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process protein destabilization regulation of protein stability regulation of biological quality positive regulation of proteasomal protein catabolic process catabolic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process cellular process cell cycle regulation of cell cycle positive regulation of cell cycle positive regulation of cellular process protein destabilization regulation of protein stability regulation of biological quality positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process metabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process positive regulation of viral genome replication positive regulation of viral process viral life cycle regulation of viral life cycle regulation of viral process viral genome replication viral process regulation of viral genome replication cellular response to stimulus response to stimulus DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair response to light stimulus cellular response to environmental stimulus cellular response to light stimulus cellular response to radiation response to UV UV-damage excision repair response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV	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 catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex Golgi apparatus endomembrane system
A, B, C, D	Protein Vpr	-	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host cell cycle progression symbiont-mediated arrest of host cell cycle during G2/M transition modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction viral penetration into host nucleus intracellular transport of virus viral process viral life cycle transport of virus symbiont entry into host cell symbiont entry into host transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization symbiont-mediated activation of host programmed cell death symbiont-mediated activation of host apoptosis symbiont-mediated perturbation of host programmed cell death disruption of cell in another organism symbiont-mediated perturbation of host apoptosis disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis	host cellular component cellular anatomical structure host cell other organism part host extracellular region host intracellular membrane-bounded organelle host intracellular part host cell part host intracellular region host cell nucleus host intracellular organelle virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth F], F [auth G]	IPR004806	UV excision repair protein Rad23	Family
E [auth F], F [auth G]	IPR036353	XPC-binding domain superfamily	Homologous Superfamily
E [auth F], F [auth G]	IPR015360	XPC-binding domain	Domain
E [auth F], F [auth G]	IPR015940	Ubiquitin-associated domain	Domain
E [auth F], F [auth G]	IPR041811	RAD23A/RAD23B, UBA1 domain	Domain
E [auth F], F [auth G]	IPR000626	Ubiquitin-like domain	Domain
E [auth F], F [auth G]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
E [auth F], F [auth G]	IPR009060	UBA-like superfamily	Homologous Superfamily
E [auth F], F [auth G]	IPR006636	Heat shock chaperonin-binding	Domain
A, B, C, D	IPR000012	Retroviral VpR/VpX protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth F], F [auth G]	Pharos: P54725	bipolar disorder Duchenne muscular dystrophy hereditary diffuse gastric adenocarcinoma ovarian cancer Disease Exacerbation gastric cancer psoriasis gastric neoplasm osteosarcoma

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.