SAXSdb — 8vud

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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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–190	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–190	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

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 8VUD	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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
6NIL cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex Deposited 2018-12-29	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 Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 185–373（189 aa） Fragment：C-terminal domain Chain D 185–373（189 aa） Fragment：C-terminal domain Chain G 185–373（189 aa） Fragment：C-terminal domain Chain J 185–373（189 aa） Fragment：C-terminal domain	Mutation：Y196D, H247G, C248R, F302K, W310K, Y314A, Q315A, K355D, K358D, F363D Mutation：Y196D, H247G, C248R, F302K, W310K, Y314A, Q315A, K355D, K358D, F363D Mutation：Y196D, H247G, C248R, F302K, W310K, Y314A, Q315A, K355D, K358D, F363D Mutation：Y196D, H247G, C248R, F302K, W310K, Y314A, Q315A, K355D, K358D, F363D	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

9 other PDB entries and 18 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 8–197； UniProt 1–190 Author chain B； PDBConstruct 8–197； UniProt 1–190

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8vud
Deposition date deposition_date	2024-01-29
Structure title title	Crystal structure of APOBEC3F-CD1
Keywords keywords	APOBEC3F, HIV, Cytidine Deaminases, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	24.11 Å
Radius of gyration Rg (electron density) rg_electron	22.87 Å
Forward intensity I(0) i0	34388300.00
Molecular weight molecular_weight	44476.0 kDa
Excluded volume excluded_volume	55186 Å³
Envelope volume envelope_volume	70143 Å³
Hydration-shell volume shell_volume	25406 Å³
Envelope diameter envelope_diameter	81.3 Å
Shell Rg shell_rg	29.92 Å
Envelope Rg envelope_rg	22.49 Å
Shape Rg shape_rg	22.81 Å
Total Rg total_rg	23.87 Å
Total atoms total_atoms	3122
Residues n_residues	370
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	75.9 Å
Rg (real space) rg_real	23.97 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	3.4390e+07
I(0) uncertainty (real space) i0_real_error	4.1390e+05
Rg (reciprocal space) rg_reciprocal	24.01 Å
I(0) (reciprocal space) i0_reciprocal	34390000.0000
Solution quality estimate total_estimate	0.9039
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.8 Å
Skewness Skewness skewness	0.129
Kurtosis Kurtosis kurtosis	-0.550
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7354000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.953

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA dC->dU-editing enzyme APOBEC-3F
Molecular weight formula_weight	23247.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3139

GPGGSGGMKPHFRNTVERMDRDTFSYNFYNEPILARRNTVWLCYEVKTKGPSRPRLDAKIFRGQVYSQPEHHAEMCFLSWFCGNQLPADKCFQITWFVSWTPCPDCVAKLAEFLAEHPNVTLTISAARLYYYSERDYRRALCRLSQAGARVKIMDDEEFAYCWENFVDSEGQPFMPWYKFDDNYAFLHRTLKEILRN

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 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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8. Citations (1)

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Unit-cell length a length_a	124.388 Å
Unit-cell length b length_b	124.388 Å
Unit-cell length c length_c	64.011 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 6
Space-group number int_tables_number	168
Crystal system crystal_system	—

Resolution resolution	2.599 Å
Low-resolution limit resolution_low	41.213 Å
R factor r_factor	0.1844
R_work r_work	0.1783
R_free r_free	0.2386

fit	/app/data/saxs_computation/vu/8vud/8vud.fit
pddf	/app/data/pr_computation/vu/8vud/8vud.pr.out
profile	/app/data/saxs_computation/vu/8vud/8vud.dat

Crystal structure of APOBEC3F-CD1

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

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

Refinement Refinement

Diffraction experiment Diffraction