SAXSdb — 3wus

▼

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 187–373	Fragment：C-TERMINAL DOMAIN, UNP RESIDUES 187-373	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 187–373	Fragment：C-TERMINAL DOMAIN, UNP RESIDUES 187-373	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

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 3WUS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4IOU Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F Deposited 2013-01-08	Different construct Different mutation/modification 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 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 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 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 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 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 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 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
8VUD Crystal structure of APOBEC3F-CD1 Deposited 2024-01-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 ligand/ion 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 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 4–190； UniProt 187–373 Author chain B； PDBConstruct 4–190； UniProt 187–373

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3wus
Deposition date deposition_date	2014-05-02
Structure title title	Crystal Structure of the Vif-Binding Domain of Human APOBEC3F
Keywords keywords	;APOBEC3F, A3F, Zinc binding, Hydrolase, antiviral enzyme, CYTIDINE DEAMINASE, DNA binding, HIV-1 VIF, single-stranded polynucleotide ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	25.55 Å
Radius of gyration Rg (electron density) rg_electron	24.57 Å
Forward intensity I(0) i0	32606200.00
Molecular weight molecular_weight	44353.0 kDa
Excluded volume excluded_volume	55325 Å³
Envelope volume envelope_volume	68589 Å³
Hydration-shell volume shell_volume	23663 Å³
Envelope diameter envelope_diameter	82.5 Å
Shell Rg shell_rg	31.37 Å
Envelope Rg envelope_rg	24.51 Å
Shape Rg shape_rg	24.56 Å
Total Rg total_rg	25.37 Å
Total atoms total_atoms	3132
Residues n_residues	368
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

▼

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

Maximum dimension Dmax dmax	80.5 Å
Rg (real space) rg_real	25.58 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	3.2610e+07
I(0) uncertainty (real space) i0_real_error	4.8580e+05
Rg (reciprocal space) rg_reciprocal	25.58 Å
I(0) (reciprocal space) i0_reciprocal	32610000.0000
Solution quality estimate total_estimate	0.9029
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.321
Kurtosis Kurtosis kurtosis	-0.586
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6283000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.960

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

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	22868.8 kDa
EC 编号 ec_number	3.5.4.-
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

MNPILRNPMEAMYPHIFYFHFKNLRKAYGRNESWLCFTMEVVKHHSPVSWKRGVFRNQVDPETHCHAERCFLSWFCDDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIFTARLYYFWDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPWKGLKYNFLFLDSKLQEILE

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	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	7

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3wusa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.6 — apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains

Domain ID domain_id	d3wusb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.6 — apolipoprotein B messenger RNA-editing enzyme catalytic (APOBEC) cytidine deaminase domains

▶

8. Citations (1)

▶

Unit-cell length a length_a	117.294 Å
Unit-cell length b length_b	117.294 Å
Unit-cell length c length_c	78.960 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.540 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2027
R_work r_work	0.1998
R_free r_free	0.2565

fit	/app/data/saxs_computation/wu/3wus/3wus.fit
pddf	/app/data/pr_computation/wu/3wus/3wus.pr.out
profile	/app/data/saxs_computation/wu/3wus/3wus.dat

Crystal Structure of the Vif-Binding Domain of Human APOBEC3F

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