5b56

Crystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Importin-Alpha2 complex

Method: X-RAY DIFFRACTION Dmax: 134.0 Å Quality: GOOD

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

Importin subunit alpha-1

Mus musculus

UniProt P52293

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 70–529 Chain B; UniProt 70–529 Fragment:UNP RESIDUES 70-529 Protein Vpr × 4 (Q73369) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.2;293 K;50MM MES, 100MM AMMONIUM SULFATE, 10MM MGCL2, 20-23%(W/V) PEG8000, 5MM DTT Resolution 2.30 Å R-free 0.226

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.

150 other PDB entries and 151 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IMA1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–460; UniProt 70–529 Author chain B; PDBConstruct 1–460; UniProt 70–529

Protein Vpr

OrganismNot specified

UniProt Q73369

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 85–96 Chain D; UniProt 85–96 Chain E; UniProt 85–96 Chain F; UniProt 85–96 Fragment:C-TERMINAL DOMAIN, UNP RESIDUES 85-96 Importin subunit alpha-1 × 2 (P52293) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.2;293 K;50MM MES, 100MM AMMONIUM SULFATE, 10MM MGCL2, 20-23%(W/V) PEG8000, 5MM DTT Resolution 2.30 Å R-free 0.226

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.

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VPR_HV1B9
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–12; UniProt 85–96 Author chain D; PDBConstruct 1–12; UniProt 85–96 Author chain E; PDBConstruct 1–12; UniProt 85–96 Author chain F; PDBConstruct 1–12; UniProt 85–96

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 5b56

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5b56
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5b56
Deposition date deposition_date2016-04-25
Structure title titleCrystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Importin-Alpha2 complex
Keywords keywordsARM REPEAT, ALL ALPHA PROTEIN, NUCLEAR IMPORT, IMPORTIN-BETA, NLS-CARGO, PROTEIN TRANSPORT-VIRAL PROTEIN COMPLEX; PROTEIN TRANSPORT/VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.52
Radius of gyration Rg (electron density) rg_electron39.55
Forward intensity I(0) i0146050000.00
Molecular weight molecular_weight98785.0 kDa
Excluded volume excluded_volume124430 ų
Envelope volume envelope_volume172020 ų
Hydration-shell volume shell_volume37880 ų
Envelope diameter envelope_diameter128.6
Shell Rg shell_rg42.89
Envelope Rg envelope_rg38.34
Shape Rg shape_rg39.57
Total Rg total_rg39.72
Total atoms total_atoms14047
Residues n_residues909
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 dmax134.0
Rg (real space) rg_real39.72
Rg uncertainty (real space) rg_real_error1.23
I(0) (real space) i0_real1.4610e+08
I(0) uncertainty (real space) i0_real_error2.4780e+06
Rg (reciprocal space) rg_reciprocal39.61
I(0) (reciprocal space) i0_reciprocal146000000.0000
Solution quality estimate total_estimate0.7934
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.9
Skewness Skewness skewness0.283
Kurtosis Kurtosis kurtosis-0.726
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11660000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.771; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5b56A00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id5b56B00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant

8. Citations (1)

9. Files and Curves (10)