6zx9

Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396)

Method: X-RAY DIFFRACTION Dmax: 142.1 Å Quality: GOOD

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

DNA damage-binding protein 1

Homo sapiens

UniProt Q16531

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–1140 Not recorded DDB1- and CUL4-associated factor 1 × 1 (Q9Y4B6) Vpr protein fused to T4 lysozyme × 1 (P00720,A4UDG5) GOL GLYCEROL × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2. Resolution 2.52 Å R-free 0.260

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.

202 other PDB entries and 290 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DDB1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–1142; UniProt 1–1140

DDB1- and CUL4-associated factor 1

Homo sapiens

UniProt Q9Y4B6

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1046–1396 Not recorded DNA damage-binding protein 1 × 1 (Q16531) Vpr protein fused to T4 lysozyme × 1 (P00720,A4UDG5) GOL GLYCEROL × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2. Resolution 2.52 Å R-free 0.260

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.

46 other PDB entries and 60 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DCAF1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–352; UniProt 1046–1396

Vpr protein fused to T4 lysozyme

Simian immunodeficiency virus

UniProt A4UDG5

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–92 Not recorded DNA damage-binding protein 1 × 1 (Q16531) DDB1- and CUL4-associated factor 1 × 1 (Q9Y4B6) GOL GLYCEROL × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2. Resolution 2.52 Å R-free 0.260

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.

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

View Construct and Data Evidence
UniProt name A4UDG5_SIV
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 167–258; UniProt 1–92

Vpr protein fused to T4 lysozyme

Simian immunodeficiency virus

UniProt P00720

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 2–164 Not recorded DNA damage-binding protein 1 × 1 (Q16531) DDB1- and CUL4-associated factor 1 × 1 (Q9Y4B6) GOL GLYCEROL × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2. Resolution 2.52 Å R-free 0.260

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.

721 other PDB entries and 846 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENLYS_BPT4
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–163; UniProt 2–164

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

SAXS profile for 6zx9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6zx9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6zx9
Deposition date deposition_date2020-07-29
Structure title titleCrystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396)
Keywords keywordsviral protein Vpr, viral hijacking of human ubiquitin ligase CRL4, DDB1, DCAF1, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier41.73
Radius of gyration Rg (electron density) rg_electron41.30
Forward intensity I(0) i0563760000.00
Molecular weight molecular_weight193450.0 kDa
Excluded volume excluded_volume241840 ų
Envelope volume envelope_volume324250 ų
Hydration-shell volume shell_volume66142 ų
Envelope diameter envelope_diameter151.7
Shell Rg shell_rg45.98
Envelope Rg envelope_rg40.95
Shape Rg shape_rg41.30
Total Rg total_rg41.56
Total atoms total_atoms13597
Residues n_residues1715
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax142.1
Rg (real space) rg_real41.75
Rg uncertainty (real space) rg_real_error1.27
I(0) (real space) i0_real5.6380e+08
I(0) uncertainty (real space) i0_real_error9.7430e+06
Rg (reciprocal space) rg_reciprocal41.73
I(0) (reciprocal space) i0_reciprocal563700000.0000
Solution quality estimate total_estimate0.8716
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary52.3
Skewness Skewness skewness0.396
Kurtosis Kurtosis kurtosis-0.166
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha94350000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.841

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6zx9A01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6zx9A02
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6zx9B01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6zx9C01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40

8. Citations (1)

9. Files and Curves (10)