Annotations: 8J62

Cryo-EM structure of APOBEC3G-Vif complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Cullin_AB	e8j62A1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.2)
G [auth B]	Cullin_AB	e8j62B1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.2)
B [auth C]	Cullin_AB	e8j62C1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.2)
D [auth E]	Cullin_AB	e8j62E1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.2)
H [auth G]	Cullin_AB	e8j62G1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.2)
J [auth I]	Cullin_AB	e8j62I1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.2)
C [auth D]	Cullin_AB	e8j62D1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.2)
E [auth F]	Spt4	e8j62F1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Spt4	ECOD (v294.2)
I [auth H]	Cullin_AB	e8j62H1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.2)
K [auth J]	Cullin_AB	e8j62J1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, G [auth B]	PF18782	APOBEC3, cytosine deaminase domain (APOBEC3)	APOBEC3, cytosine deaminase domain	This domain is found in APOBEC3 (A/B/C/D/F/G) proteins and is homologous to known CMP/dCMP-type deaminase domains. APOBEC3 proteins are a family of cytidine deaminases that play a crucial role in the host's intrinsic immunity by restricting the repli ...	This domain is found in APOBEC3 (A/B/C/D/F/G) proteins and is homologous to known CMP/dCMP-type deaminase domains. APOBEC3 proteins are a family of cytidine deaminases that play a crucial role in the host's intrinsic immunity by restricting the replication of viruses - particularly retroviruses like HIV-1 - and inhibiting the transposition of endogenous elements such as LINE-1. In humans, there are seven APOBEC3 genes: A3A, A3B, A3C, A3D, A3F, A3G, and A3H, all located on chromosome 22. Each protein contains one or two zinc-binding domains, which are essential for their catalytic activity - the conversion of cytosine to uracil in single-stranded DNA, and sometimes RNA [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, G [auth B]	APOBEC3G	RNA binding binding nucleic acid binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds dCTP deaminase activity cation binding transition metal ion binding zinc ion binding ion binding RNA binding binding nucleic acid binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds dCTP deaminase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding identical protein binding protein binding	regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition macromolecule biosynthetic process regulation of gene expression regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process retrotransposition regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression transposition 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 transposable element silencing regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process cytidine to uridine editing RNA metabolic process primary metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA modification base conversion or substitution editing macromolecule modification negative regulation of viral process regulation of viral process viral process 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 DNA cytosine deamination DNA metabolic process DNA deamination DNA modification defense response to virus antiviral innate immune response response to virus negative regulation of viral genome replication viral life cycle regulation of viral life cycle viral genome replication regulation of viral genome replication regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus regulation of defense response to virus regulation of response to stimulus regulation of response to stress positive regulation of defense response to virus by host regulation of defense response to virus by host regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of single stranded viral RNA replication via double stranded DNA intermediate negative regulation of RNA biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA metabolic process viral RNA genome replication negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process single stranded viral RNA replication via double stranded DNA intermediate negative regulation of RNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex apolipoprotein B mRNA editing enzyme complex catalytic complex mRNA editing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex apolipoprotein B mRNA editing enzyme complex catalytic complex mRNA editing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex P-body ribonucleoprotein complex
B [auth C], D [auth E], H [auth G], J [auth I]	Viral 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
C [auth D], E [auth F], I [auth H], K [auth J]	Core binding factor beta	transcription coactivator activity transcription regulator activity transcription coregulator activity sequence-specific DNA binding DNA binding binding nucleic acid binding	developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation protein polyubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation protein polyubiquitination primary 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 hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation immune system process anatomical structure development leukocyte differentiation RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process definitive hemopoiesis regulation of cellular process 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 biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of leukocyte differentiation CD8-positive, alpha-beta T cell activation regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation regulation of cell differentiation positive regulation of T cell differentiation positive regulation of CD8-positive, alpha-beta T cell activation regulation of cell development positive regulation of developmental process positive regulation of cell activation multicellular organism development T cell activation positive regulation of leukocyte activation alpha-beta T cell activation regulation of immune system process T cell differentiation positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development positive regulation of alpha-beta T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process positive regulation of alpha-beta T cell differentiation regulation of developmental process CD8-positive, alpha-beta T cell differentiation positive regulation of biological process positive regulation of leukocyte cell-cell adhesion regulation of alpha-beta T cell differentiation leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion alpha-beta T cell differentiation cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process regulation of lymphocyte differentiation regulation of multicellular organismal development positive regulation of cell adhesion regulation of cell adhesion positive regulation of CD8-positive, alpha-beta T cell differentiation regulation of T cell activation regulation of CD8-positive, alpha-beta T cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation regulation of CD8-positive, alpha-beta T cell activation positive regulation of lymphocyte differentiation regulation of lymphocyte activation positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process myeloid cell differentiation anatomical structure maturation cell maturation developmental maturation negative regulation of cell adhesion negative regulation of T cell differentiation negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of CD4-positive, alpha-beta T cell activation negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation negative regulation of multicellular organismal process negative regulation of CD4-positive, alpha-beta T cell differentiation negative regulation of leukocyte activation regulation of CD4-positive, alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation negative regulation of alpha-beta T cell differentiation negative regulation of lymphocyte activation CD4-positive, alpha-beta T cell activation negative regulation of cell differentiation negative regulation of developmental process negative regulation of cell activation negative regulation of cell development regulation of CD4-positive, alpha-beta T cell activation negative regulation of immune system process negative regulation of alpha-beta T cell activation	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure core-binding factor complex organelle membrane membrane-enclosed lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure core-binding factor complex organelle membrane membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
F [auth X], L [auth Y]	RNA (5'-R(CPGPGPUPUPGPAPUPUPGPUPUPUPUPAPAPCPAP*A)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, G [auth B]	IPR050610	APOBEC Cytidine Deaminase	Family
A, G [auth B]	IPR016193	Cytidine deaminase-like	Homologous Superfamily
A, G [auth B]	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A, G [auth B]	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site
B [auth C], D [auth E], H [auth G], J [auth I]	IPR000475	Retroviral Vif (Viral infectivity) protein	Family
C [auth D], E [auth F], I [auth H], K [auth J]	IPR003417	Core-binding factor, beta subunit	Family
C [auth D], E [auth F], I [auth H], K [auth J]	IPR036552	Core-binding factor, beta subunit superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, G [auth B]	: Q9HC16	Sjogren syndrome ulcerative colitis adrenal cortex carcinoma B-cell chronic lymphocytic leukemia Crohn disease invasive ductal breast carcinoma malignant glioma ovarian cancer plasma cell myeloma subependymal giant cell astrocytoma AIDS breast cancer cutaneous lupus erythematosus lung cancer malignant mesothelioma Sjogren syndrome ulcerative colitis adrenal cortex carcinoma B-cell chronic lymphocytic leukemia Crohn disease invasive ductal breast carcinoma malignant glioma ovarian cancer plasma cell myeloma subependymal giant cell astrocytoma AIDS breast cancer cutaneous lupus erythematosus lung cancer malignant mesothelioma pilocytic astrocytoma psoriasis tuberculosis astrocytic tumor chronic kidney disease glioblastoma lung carcinoma osteosarcoma pituitary cancer
C [auth D], E [auth F], I [auth H], K [auth J]	: Q13951	acute myeloid leukemia cleft palate acute myelomonocytic leukemia M4 Bone Diseases, Developmental malignant glioma myopathy ovarian cancer atypical teratoid rhabdoid tumor congenital heart disease glioblastoma juvenile dermatomyositis lymphoplasmacytic lymphoma pilocytic astrocytoma large cell medulloblastoma malignant ependymoma acute myeloid leukemia cleft palate acute myelomonocytic leukemia M4 Bone Diseases, Developmental malignant glioma myopathy ovarian cancer atypical teratoid rhabdoid tumor congenital heart disease glioblastoma juvenile dermatomyositis lymphoplasmacytic lymphoma pilocytic astrocytoma large cell medulloblastoma malignant ependymoma medulloblastoma osteosarcoma ulcerative colitis amyotrophic lateral sclerosis cancer Down syndrome IgA glomerulonephritis

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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.