3nc0

Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal II)

Method: X-RAY DIFFRACTION Dmax: 178.3 Å Quality: GOOD

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

Exportin-1

Mus musculus

UniProt Q6P5F9

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 1–1071 Chain D; UniProt 1–1071 Not recorded Snurportin-1 × 1 (O95149) GTP-binding nuclear protein Ran × 2 (P62826) GOL GLYCEROL × 8 PEG DI(HYDROXYETHYL)ETHER × 11 IPH PHENOL × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293 K;0.1 M Tris/HCl, 16% (w/v) PEG 1000, 2 mM phenol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.295
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–1071 Chain D; UniProt 1–1071 Not recorded Snurportin-1 × 2 (O95149) GTP-binding nuclear protein Ran × 2 (P62826) GOL GLYCEROL × 10 PEG DI(HYDROXYETHYL)ETHER × 11 IPH PHENOL × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293 K;0.1 M Tris/HCl, 16% (w/v) PEG 1000, 2 mM phenol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.295

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.

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

View Construct and Data Evidence
UniProt name XPO1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–1073; UniProt 1–1071 Author chain D; PDBConstruct 3–1073; UniProt 1–1071

Snurportin-1

Homo sapiens

UniProt O95149

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 15–360 Not recorded Exportin-1 × 2 (Q6P5F9) GTP-binding nuclear protein Ran × 2 (P62826) GOL GLYCEROL × 8 PEG DI(HYDROXYETHYL)ETHER × 11 IPH PHENOL × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293 K;0.1 M Tris/HCl, 16% (w/v) PEG 1000, 2 mM phenol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.295
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 15–360 Chain E; UniProt 15–360 Not recorded Exportin-1 × 2 (Q6P5F9) GTP-binding nuclear protein Ran × 2 (P62826) GOL GLYCEROL × 10 PEG DI(HYDROXYETHYL)ETHER × 11 IPH PHENOL × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293 K;0.1 M Tris/HCl, 16% (w/v) PEG 1000, 2 mM phenol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.295

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.

10 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPN1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 17–362; UniProt 15–360 Author chain E; PDBConstruct 17–362; UniProt 15–360

GTP-binding nuclear protein Ran

Homo sapiens

UniProt P62826

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 5–180 Chain F; UniProt 5–180 Mutation:Q69L Exportin-1 × 2 (Q6P5F9) Snurportin-1 × 1 (O95149) GOL GLYCEROL × 8 PEG DI(HYDROXYETHYL)ETHER × 11 IPH PHENOL × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293 K;0.1 M Tris/HCl, 16% (w/v) PEG 1000, 2 mM phenol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.295
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 5–180 Chain F; UniProt 5–180 Mutation:Q69L Exportin-1 × 2 (Q6P5F9) Snurportin-1 × 2 (O95149) GOL GLYCEROL × 10 PEG DI(HYDROXYETHYL)ETHER × 11 IPH PHENOL × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;293 K;0.1 M Tris/HCl, 16% (w/v) PEG 1000, 2 mM phenol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.90 Å R-free 0.295

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.

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

View Construct and Data Evidence
UniProt name RAN_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–176; UniProt 5–180 Author chain F; PDBConstruct 1–176; UniProt 5–180

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 3nc0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3nc0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3nc0
Deposition date deposition_date2010-06-04
Structure title titleCrystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal II)
Keywords keywordsprotein transport, GTP-binding protein-transport protein complex; GTP-binding protein/transport protein
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier53.21
Radius of gyration Rg (electron density) rg_electron53.09
Forward intensity I(0) i01655530000.00
Molecular weight molecular_weight349050.0 kDa
Excluded volume excluded_volume440540 ų
Envelope volume envelope_volume644730 ų
Hydration-shell volume shell_volume100810 ų
Envelope diameter envelope_diameter178.1
Shell Rg shell_rg56.90
Envelope Rg envelope_rg51.71
Shape Rg shape_rg53.09
Total Rg total_rg53.24
Total atoms total_atoms24542
Residues n_residues3012
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 dmax178.3
Rg (real space) rg_real53.17
Rg uncertainty (real space) rg_real_error1.62
I(0) (real space) i0_real1.6560e+09
I(0) uncertainty (real space) i0_real_error3.3280e+07
Rg (reciprocal space) rg_reciprocal53.22
I(0) (reciprocal space) i0_reciprocal1656000000.0000
Solution quality estimate total_estimate0.8798
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary59.4
Skewness Skewness skewness0.287
Kurtosis Kurtosis kurtosis-0.438
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha152000000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.765

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3nc0c_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd3nc0f_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins

CATH v4.4 (4 domains)

Domain ID domain_id3nc0B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily30 — DNA ligase/mRNA capping enzyme
Domain ID domain_id3nc0C00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3nc0E00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily30 — DNA ligase/mRNA capping enzyme
Domain ID domain_id3nc0F00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)