6nil

cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex

Method: ELECTRON MICROSCOPY D_max: 124.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA dC->dU-editing enzyme APOBEC-3F

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 185–373 Chain D； UniProt 185–373 Chain G； UniProt 185–373 Chain J； UniProt 185–373	Fragment：C-terminal domain Mutation：Y196D, H247G, C248R, F302K, W310K, Y314A, Q315A, K355D, K358D, F363D	Core-binding factor subunit beta × 4 （Q13951） Virion infectivity factor × 4 （P12504,A0A346ARH7） ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6NIL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3WUS Crystal Structure of the Vif-Binding Domain of Human APOBEC3F Deposited 2014-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 187–373（187 aa） Fragment：C-TERMINAL DOMAIN, UNP RESIDUES 187-373	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；8.5% PEG 20000, 2% Dioxane, 300mM L-Arginine HCl, 85mM Na BICINE, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.54 Å R-free 0.256
3WUS Crystal Structure of the Vif-Binding Domain of Human APOBEC3F Deposited 2014-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 187–373（187 aa） Fragment：C-TERMINAL DOMAIN, UNP RESIDUES 187-373	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；8.5% PEG 20000, 2% Dioxane, 300mM L-Arginine HCl, 85mM Na BICINE, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.54 Å R-free 0.256
4IOU Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F Deposited 2013-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 185–373（189 aa） Fragment：C-TERMINAL DOMAIN, UNP residues 185-373	Mutation：Y196D, H247G, C248R, C259A, F302D, W310K, Y314Y, Q315A, F363D, K355D, K358D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；288 K；0.1 M Tris-HCl pH 8.0, 20% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.75 Å R-free 0.233
4IOU Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F Deposited 2013-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 185–373（189 aa） Fragment：C-TERMINAL DOMAIN, UNP residues 185-373	Mutation：Y196D, H247G, C248R, C259A, F302D, W310K, Y314Y, Q315A, F363D, K355D, K358D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；288 K；0.1 M Tris-HCl pH 8.0, 20% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.75 Å R-free 0.233
4IOU Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F Deposited 2013-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 185–373（189 aa） Fragment：C-TERMINAL DOMAIN, UNP residues 185-373	Mutation：Y196D, H247G, C248R, C259A, F302D, W310K, Y314Y, Q315A, F363D, K355D, K358D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；288 K；0.1 M Tris-HCl pH 8.0, 20% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.75 Å R-free 0.233
4IOU Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F Deposited 2013-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 185–373（189 aa） Fragment：C-TERMINAL DOMAIN, UNP residues 185-373	Mutation：Y196D, H247G, C248R, C259A, F302D, W310K, Y314Y, Q315A, F363D, K355D, K358D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；288 K；0.1 M Tris-HCl pH 8.0, 20% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.75 Å R-free 0.233
4J4J Crystal structure of the APOBEC3F Vif binding domain Deposited 2013-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 218–373（156 aa） Fragment：UNP residues 218-373	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；18% (w/v) PEG 8000, 0.1 M CHES pH 9.0, 25% (w/v) glucose, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.277
4J4J Crystal structure of the APOBEC3F Vif binding domain Deposited 2013-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 218–373（156 aa） Fragment：UNP residues 218-373	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；18% (w/v) PEG 8000, 0.1 M CHES pH 9.0, 25% (w/v) glucose, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.277
5HX4 Zinc-Free APOBEC3F Catalytic Domain Crystal Structure Deposited 2016-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 185–373（189 aa） Fragment：UNP residues 185-373	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tacsimate pH5.0, PEG3350, Glycerol	Resolution 1.92 Å R-free 0.214
5HX4 Zinc-Free APOBEC3F Catalytic Domain Crystal Structure Deposited 2016-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 185–373（189 aa） Fragment：UNP residues 185-373	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tacsimate pH5.0, PEG3350, Glycerol	Resolution 1.92 Å R-free 0.214
5HX5 APOBEC3F Catalytic Domain Crystal Structure Deposited 2016-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 185–373（189 aa） Fragment：UNP residues 185-373	Mutation：Y196D, H247G, C248R, C259A, F302K, W310D, K355D, K358D, F363D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；PEG3350, MgCl2	Resolution 2.33 Å R-free 0.264
5HX5 APOBEC3F Catalytic Domain Crystal Structure Deposited 2016-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 185–373（189 aa） Fragment：UNP residues 185-373	Mutation：Y196D, H247G, C248R, C259A, F302K, W310D, K355D, K358D, F363D	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；PEG3350, MgCl2	Resolution 2.33 Å R-free 0.264
5W2M APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA Deposited 2017-06-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: dodecameric	Chain A 190–373（184 aa） Chain B 190–373（184 aa） Chain C 190–373（184 aa） Chain D 190–373（184 aa） Chain J 190–373（184 aa） Chain K 190–373（184 aa） Chain L 190–373（184 aa） Chain M 190–373（184 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.05 M HEPES, pH 7.0, 0.1 M Potassium chloride, 0.005 M Magnesium Sulfate, 15%(v/v) MPD	Resolution 3.70 Å R-free 0.267
5ZVA APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9) Deposited 2018-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: dimeric	Chain A 218–373（156 aa）	Not recorded	ZN ZINC ION × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05M sodium cacodylate, pH 6.5, and 30%(v/v) 2-methyl-2,4-pentanediol(MPD)	Resolution 2.30 Å R-free 0.208
5ZVA APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9) Deposited 2018-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 218–373（156 aa）	Not recorded	ZN ZINC ION × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05M sodium cacodylate, pH 6.5, and 30%(v/v) 2-methyl-2,4-pentanediol(MPD)	Resolution 2.30 Å R-free 0.208
5ZVB APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9) Deposited 2018-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: dimeric	Chain A 218–373（156 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05M sodium cacodylate, pH 6.5, and 30%(v/v) 2-methyl-2,4-pentanediol (MPD)	Resolution 2.00 Å R-free 0.220
5ZVB APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9) Deposited 2018-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 218–373（156 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05M sodium cacodylate, pH 6.5, and 30%(v/v) 2-methyl-2,4-pentanediol (MPD)	Resolution 2.00 Å R-free 0.220
8VUD Crystal structure of APOBEC3F-CD1 Deposited 2024-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–190（190 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris, pH 5.5, 1.8 M ammonium sulfate	Resolution 2.60 Å R-free 0.239
8VUD Crystal structure of APOBEC3F-CD1 Deposited 2024-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–190（190 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris, pH 5.5, 1.8 M ammonium sulfate	Resolution 2.60 Å R-free 0.239

9 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ABC3F_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–207； UniProt 185–373 Author chain D； PDBConstruct 19–207； UniProt 185–373 Author chain G； PDBConstruct 19–207； UniProt 185–373 Author chain J； PDBConstruct 19–207； UniProt 185–373

Core-binding factor subunit beta

Homo sapiens

UniProt Q13951

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain B； UniProt 1–151 Chain E； UniProt 1–151 Chain H； UniProt 1–151 Chain K； UniProt 1–151	Not recorded	DNA dC->dU-editing enzyme APOBEC-3F × 4 （Q8IUX4） Virion infectivity factor × 4 （P12504,A0A346ARH7） ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6NIL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CL3 MOLECULAR INSIGHTS INTO PEBP2/CBF-SMMHC ASSOCIATED ACUTE LEUKEMIA REVEALED FROM THE THREE-DIMENSIONAL STRUCTURE OF PEBP2/CBF BETA Deposited 1999-05-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–141（138 aa） Fragment：BETA SUBUNIT	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K NMR sample composition 96% WATER/4% D2O	Resolution not provided
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1E50 AML1/CBFbeta complex Deposited 2000-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.287
1H9D Aml1/cbf-beta/dna complex Deposited 2001-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.271
1H9D Aml1/cbf-beta/dna complex Deposited 2001-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain D 2–135（134 aa） Fragment：HETERODIMERISATION DOMAIN RESIDUES 2-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.271
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain a 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain 6 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain k 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain N 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain L 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain c 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain i 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain o 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain u 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
4N9F Crystal structure of the Vif-CBFbeta-CUL5-ElOB-ElOC pentameric complex Deposited 2013-10-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain 0 1–170（170 aa） Fragment：UNP residues 1-170	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.22M potassium sulfate, 18% (w/v) polyethylene glycol (PEG) 3350, 100mM Tris HCl, pH 8.0., VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 3.30 Å R-free 0.324
6P59 Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex Deposited 2019-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–165（165 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；MES (pH 6), PEG 6000, Dichloromethane	Resolution 2.94 Å R-free 0.268
6P59 Crystal structure of SIVrcm Vif-CBFbeta-ELOB-ELOC complex Deposited 2019-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–165（165 aa）	Not recorded	ZN ZINC ION × 1 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；MES (pH 6), PEG 6000, Dichloromethane	Resolution 2.94 Å R-free 0.268
6VGD Crystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0	Resolution 4.20 Å R-free 0.293
6VGE Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), in complex with 16mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa） Fragment：DNA binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0	Resolution 4.25 Å R-free 0.317
6VGG Crystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC Deposited 2020-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 1–142（142 aa）	Not recorded	QWP mithramycin × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.3 M K/Na Tartrate, 50 mM Hepes, pH 7.0, soaked in 1 mM mithramycin-Mg	Resolution 4.31 Å R-free 0.285
8CX0 Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex Deposited 2022-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 5 PDB declaration: hexameric	Chain C 1–182（182 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8CX1 Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 1 Deposited 2022-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain C 1–182（182 aa） Chain H 1–182（182 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8CX2 Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2 Deposited 2022-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain C 1–182（182 aa） Chain H 1–182（182 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8E40 Full-length APOBEC3G in complex with HIV-1 Vif, CBF-beta, and fork RNA Deposited 2022-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 1–157（157 aa） Fragment：UNP residues 1-157	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
8FVI Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5 Deposited 2023-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain 0 1–157（157 aa） Fragment：UNP residues 1-157	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8FVJ Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5 Deposited 2023-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain 0 1–157（157 aa） Fragment：UNP residues 1-157 Chain 5 1–157（157 aa） Fragment：UNP residues 1-157	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
8H0I Cryo-EM structure of APOBEC3G-Vif complex Deposited 2022-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain D 1–156（156 aa） Chain F 1–156（156 aa） Chain H 1–156（156 aa） Chain J 1–156（156 aa）	Not recorded	ZN ZINC ION × 4 CL CHLORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.80 Å
8J62 Cryo-EM structure of APOBEC3G-Vif complex Deposited 2023-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain D 1–156（156 aa） Chain F 1–156（156 aa） Chain H 1–156（156 aa） Chain J 1–156（156 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.50 Å
8SZK The cryo-EM structure of PPP2R5A/HIV-1 Vif/CBFb/EloB/EloC complex Deposited 2023-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–187（187 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
9E93 Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H Deposited 2024-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: decameric	Chain o 1–170（170 aa） Chain s 1–170（170 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
9E9V Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H Deposited 2024-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: 13-meric	Chain o 1–170（170 aa） Chain s 1–170（170 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å

19 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PEBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–151； UniProt 1–151 Author chain E； PDBConstruct 1–151； UniProt 1–151 Author chain H； PDBConstruct 1–151； UniProt 1–151 Author chain K； PDBConstruct 1–151； UniProt 1–151

Virion infectivity factor

Human immunodeficiency virus 1

UniProt A0A346ARH7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain C； UniProt 158–176 Chain F； UniProt 158–176 Chain I； UniProt 158–176 Chain L； UniProt 158–176	Not recorded	DNA dC->dU-editing enzyme APOBEC-3F × 4 （Q8IUX4） Core-binding factor subunit beta × 4 （Q13951） ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A346ARH7_9HIV1
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 120–138； UniProt 158–176 Author chain F； PDBConstruct 120–138； UniProt 158–176 Author chain I； PDBConstruct 120–138； UniProt 158–176 Author chain L； PDBConstruct 120–138； UniProt 158–176

Virion infectivity factor

Human immunodeficiency virus 1

UniProt P12504

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain C； UniProt 1–113 Chain F； UniProt 1–113 Chain I； UniProt 1–113 Chain L； UniProt 1–113	Not recorded	DNA dC->dU-editing enzyme APOBEC-3F × 4 （Q8IUX4） Core-binding factor subunit beta × 4 （Q13951） ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6NIL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MA9 HIV-1 Vif SOCS-box and Elongin BC solution structure Deposited 2013-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 139–174（36 aa） Fragment：UNP residues 139-174	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.2 mM [U-99% 13C; U-99% 15N] Vif SOCS, 0.2 mM Elongin B, 0.2 mM Elongin C, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.2 mM Vif SOCS, 0.2 mM [U-99% 13C; U-99% 15N] Elongin B, 0.2 mM [U-99% 13C; U-99% 15N] Elongin C, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.2 mM Vif SOCS, 0.2 mM [U-99% 13C; U-99% 15N] Elongin B, 0.2 mM [U-99% 13C; U-99% 15N] Elongin C, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3DCG Crystal Structure of the HIV Vif BC-box in Complex with Human ElonginB and ElonginC Deposited 2008-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 139–176（38 aa） Fragment：UNP residues 139-176	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.1M Tris HCl pH 7.0, 40% PEG 350 MME, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.232
3DCG Crystal Structure of the HIV Vif BC-box in Complex with Human ElonginB and ElonginC Deposited 2008-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 139–176（38 aa） Fragment：UNP residues 139-176	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.1M Tris HCl pH 7.0, 40% PEG 350 MME, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.40 Å R-free 0.232
8FVI Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5 Deposited 2023-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain 1 1–176（176 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8FVJ Dimeric form of HIV-1 Vif in complex with human CBF-beta, ELOB, ELOC, and CUL5 Deposited 2023-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain 1 1–176（176 aa） Chain 6 1–176（176 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
8SZK The cryo-EM structure of PPP2R5A/HIV-1 Vif/CBFb/EloB/EloC complex Deposited 2023-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 1–176（176 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
9E93 Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H Deposited 2024-11-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: decameric	Chain p 1–176（176 aa） Chain t 1–176（176 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
9E9V Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H Deposited 2024-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: 13-meric	Chain p 1–176（176 aa） Chain t 1–176（176 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VIF_HV1N5
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–113； UniProt 1–113 Author chain F； PDBConstruct 1–113； UniProt 1–113 Author chain I； PDBConstruct 1–113； UniProt 1–113 Author chain L； PDBConstruct 1–113； UniProt 1–113

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6nil
Deposition date deposition_date	2018-12-29
Structure title title	cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex
Keywords keywords	Human antiviral restriction factor, HIV viral protein, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	40.35 Å
Radius of gyration Rg (electron density) rg_electron	39.37 Å
Forward intensity I(0) i0	717429000.00
Molecular weight molecular_weight	215610.0 kDa
Excluded volume excluded_volume	267990 Å³
Envelope volume envelope_volume	382110 Å³
Hydration-shell volume shell_volume	77946 Å³
Envelope diameter envelope_diameter	126.7 Å
Shell Rg shell_rg	47.68 Å
Envelope Rg envelope_rg	38.16 Å
Shape Rg shape_rg	39.35 Å
Total Rg total_rg	39.91 Å
Total atoms total_atoms	15220
Residues n_residues	1800
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	124.9 Å
Rg (real space) rg_real	40.12 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	7.1740e+08
I(0) uncertainty (real space) i0_real_error	1.0430e+07
Rg (reciprocal space) rg_reciprocal	40.35 Å
I(0) (reciprocal space) i0_reciprocal	717600000.0000
Solution quality estimate total_estimate	0.8932
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.4 Å
Skewness Skewness skewness	0.068
Kurtosis Kurtosis kurtosis	-0.487
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	223300000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA dC->dU-editing enzyme APOBEC-3F
Molecular weight formula_weight	24433.3 kDa
EC 编号 ec_number	3.5.4.38
Mutation mutation	Y196D, H247G, C248R, F302K, W310K, Y314A, Q315A, K355D, K358D, F363D
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	15220

MGSSHHHHHHSQDPNSMGKEILRNPMEAMDPHIFYFHFKNLRKAYGRNESWLCFTMEVVKHHSPVSWKRGVFRNQVDPETGRHAERCFLSWFCDDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFKDTDAAEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPWDGLDYNFLDLDSKLQEILE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Core-binding factor subunit beta
Molecular weight formula_weight	17851.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQEDALAQQAFEEARRRTR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Virion infectivity factor
Molecular weight formula_weight	16736.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

MENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDEASEGSQIKPPLPSVRKLTEDRWNK

来源 Source

来源生物 organism	Human immunodeficiency virus 1
通用名 common_name	HIV-1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6nilB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	250 — Polyomavirus Enhancer Binding Protein 2; Chain: A;
Homologous superfamily homologous superfamily	10 — Core binding factor, beta subunit

Domain ID domain_id	6nilE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	250 — Polyomavirus Enhancer Binding Protein 2; Chain: A;
Homologous superfamily homologous superfamily	10 — Core binding factor, beta subunit

Domain ID domain_id	6nilH00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	250 — Polyomavirus Enhancer Binding Protein 2; Chain: A;
Homologous superfamily homologous superfamily	10 — Core binding factor, beta subunit

Domain ID domain_id	6nilK00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	250 — Polyomavirus Enhancer Binding Protein 2; Chain: A;
Homologous superfamily homologous superfamily	10 — Core binding factor, beta subunit

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	337256

fit	/app/data/saxs_computation/ni/6nil/6nil.fit
pddf	/app/data/pr_computation/ni/6nil/6nil.pr.out
profile	/app/data/saxs_computation/ni/6nil/6nil.dat

cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA dC->dU-editing enzyme APOBEC-3F

State in the Current Structure

Other States of the Same Protein in the Database

Core-binding factor subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Virion infectivity factor

State in the Current Structure

Other States of the Same Protein in the Database

Virion infectivity factor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)