3DCG | pdb_00003dcg

Crystal Structure of the HIV Vif BC-box in Complex with Human ElonginB and ElonginC

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)
B	d3dcgb_	Alpha and beta proteins (a+b)	POZ domain	POZ domain	BTB/POZ domain	Elongin C	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3dcgd_	Alpha and beta proteins (a+b)	POZ domain	POZ domain	BTB/POZ domain	Elongin C	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3dcga_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Elongin B	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3dcgc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Elongin B	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)
A	SCOP2B Superfamily	Ubiquitin-like	8038575	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8038575	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)
E	Flavi_NS2B	e3dcgE01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: Flavi_NS2B	ECOD (develop294)
B	Polyketide_cyc2	e3dcgB1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Polyketide_cyc2	ECOD (develop294)
D	Polyketide_cyc2	e3dcgD1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Polyketide_cyc2	ECOD (develop294)
A	S4	e3dcgA1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: S4	ECOD (develop294)
C	RasGEF	e3dcgC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
D	3.30.710.10	Alpha Beta	2-Layer Sandwich	Potassium Channel Kv1.1	Chain A	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF03931	Skp1 family, tetramerisation domain (Skp1_POZ)	Skp1 family, tetramerisation domain		Domain
A, 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
E, F	Virion infectivity factor	RNA binding binding nucleic acid binding	viral process viral life cycle	virion component cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane other organism part host intracellular part host cell cytoplasm host intracellular region
B, D	Transcription elongation factor B polypeptide 1	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding protein-macromolecule adaptor activity molecular adaptor activity	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of macromolecule metabolic process miRNA metabolic process RNA catabolic process regulation of biological process negative regulation of metabolic process nucleobase-containing compound catabolic process miRNA-mediated post-transcriptional gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of miRNA-mediated gene silencing negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing nucleic acid catabolic process regulation of macromolecule biosynthetic process negative regulation of post-transcriptional gene silencing regulation of metabolic process positive regulation of biological process RNA metabolic process regulation of miRNA-mediated gene silencing negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of gene silencing by regulatory ncRNA biological regulation regulation of macromolecule metabolic process miRNA catabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing nucleic acid metabolic process target-directed miRNA degradation regulatory ncRNA-mediated gene silencing regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of gene expression ubiquitin-dependent protein catabolic process via the C-end degron rule pathway proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process nucleobase-containing compound biosynthetic process DNA-templated transcription initiation RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription 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 protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol cullin-RING ubiquitin ligase complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex Cul5-RING ubiquitin ligase complex Cul2-RING ubiquitin ligase complex
A, C	Transcription elongation factor B polypeptide 2	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of macromolecule metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of macromolecule metabolic process miRNA metabolic process RNA catabolic process regulation of biological process negative regulation of metabolic process primary metabolic process nucleobase-containing compound catabolic process miRNA-mediated post-transcriptional gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of miRNA-mediated gene silencing negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of post-transcriptional gene silencing regulation of metabolic process catabolic process positive regulation of biological process RNA metabolic process regulation of miRNA-mediated gene silencing macromolecule catabolic process negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of gene silencing by regulatory ncRNA biological regulation regulation of macromolecule metabolic process miRNA catabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing nucleic acid metabolic process target-directed miRNA degradation regulatory ncRNA-mediated gene silencing regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of gene expression ubiquitin-dependent protein catabolic process via the C-end degron rule pathway proteasomal protein catabolic process 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 protein metabolic process nucleobase-containing compound biosynthetic process DNA-templated transcription initiation RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of protein metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein 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 protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle elongin complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol cytoplasmic ubiquitin ligase complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex VCB complex cullin-RING ubiquitin ligase complex Cul5-RING ubiquitin ligase complex Cul2-RING ubiquitin ligase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F	IPR000475	Retroviral Vif (Viral infectivity) protein	Family
B, D	IPR016073	SKP1 component, POZ domain	Domain
B, D	IPR001232	S-phase kinase-associated protein 1-like	Family
B, D	IPR039948	Elongin-C	Family
B, D	IPR011333	SKP1/BTB/POZ domain superfamily	Homologous Superfamily
A, C	IPR000626	Ubiquitin-like domain	Domain
A, C	IPR039049	Elongin B	Family
A, C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: Q15369	papillary renal cell carcinoma sarcomatoid renal cell carcinoma collecting duct carcinoma chromophobe renal cell carcinoma renal cell carcinoma astrocytic tumor clear cell renal carcinoma dermatomyositis breast cancer invasive ductal breast carcinoma plasma cell myeloma Conventional (Clear Cell) Renal Cell Carcinoma ovarian cancer
A, C	Pharos: Q15370	acute myeloid leukemia ovarian cancer diabetes mellitus plasma cell myeloma lymphoplasmacytic lymphoma

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.