3wyf

Crystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex

Method: X-RAY DIFFRACTION Dmax: 166.6 Å Quality: REASONABLE

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

Gsp1p

Saccharomyces cerevisiae AWRI796

UniProt E7KFU1

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–219 Mutation:Q71L Ran-specific GTPase-activating protein 2 × 1 (P40517) Exportin-1 × 1 (P30822) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;0.1M CITRATE, 17% PEG6000, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K Resolution 2.22 Å R-free 0.214
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–219 Mutation:Q71L Ran-specific GTPase-activating protein 2 × 1 (P40517) Exportin-1 × 1 (P30822) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;0.1M CITRATE, 17% PEG6000, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K Resolution 2.22 Å R-free 0.214

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name E7KFU1_YEASA
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–219; UniProt 1–219 Author chain D; PDBConstruct 1–219; UniProt 1–219

Ran-specific GTPase-activating protein 2

Saccharomyces cerevisiae S288c

UniProt P40517

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 90–327 Fragment:UNP residues 90-327 Gsp1p × 1 (E7KFU1) Exportin-1 × 1 (P30822) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;0.1M CITRATE, 17% PEG6000, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K Resolution 2.22 Å R-free 0.214
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 90–327 Fragment:UNP residues 90-327 Gsp1p × 1 (E7KFU1) Exportin-1 × 1 (P30822) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;0.1M CITRATE, 17% PEG6000, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K Resolution 2.22 Å R-free 0.214

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 YRB2_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–238; UniProt 90–327 Author chain E; PDBConstruct 1–238; UniProt 90–327

Exportin-1

Saccharomyces cerevisiae S288c

UniProt P30822

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–1084 Not recorded Gsp1p × 1 (E7KFU1) Ran-specific GTPase-activating protein 2 × 1 (P40517) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;0.1M CITRATE, 17% PEG6000, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K Resolution 2.22 Å R-free 0.214
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 1–1084 Not recorded Gsp1p × 1 (E7KFU1) Ran-specific GTPase-activating protein 2 × 1 (P40517) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;0.1M CITRATE, 17% PEG6000, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K Resolution 2.22 Å R-free 0.214

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.

69 other PDB entries and 72 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XPO1_YEAST
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 3–1049; UniProt 1–1084 Author chain F; PDBConstruct 3–1049; UniProt 1–1084

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 3wyf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3wyf
Deposition date deposition_date2014-08-26
Structure title titleCrystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex
Keywords keywordsHEAT REPEAT, NUCLEAR EXPORT, GTP-BINDING PROTEIN-GTP-BINDING PROTEIN INHIBITOR complex; GTP-BINDING PROTEIN/GTP-BINDING PROTEIN INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier49.15
Radius of gyration Rg (electron density) rg_electron49.15
Forward intensity I(0) i01250580000.00
Molecular weight molecular_weight305580.0 kDa
Excluded volume excluded_volume387120 ų
Envelope volume envelope_volume540220 ų
Hydration-shell volume shell_volume91216 ų
Envelope diameter envelope_diameter181.8
Shell Rg shell_rg53.02
Envelope Rg envelope_rg48.40
Shape Rg shape_rg49.17
Total Rg total_rg49.25
Total atoms total_atoms21532
Residues n_residues2705
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 dmax166.6
Rg (real space) rg_real50.96
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real1.2470e+09
I(0) uncertainty (real space) i0_real_error2.2060e+07
Rg (reciprocal space) rg_reciprocal49.15
I(0) (reciprocal space) i0_reciprocal1251000000.0000
Solution quality estimate total_estimate0.6850
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary57.3
Skewness Skewness skewness0.487
Kurtosis Kurtosis kurtosis-0.141
Angular range angular_range— – 0.1600 −1
Current regularization parameter α current_alpha1.3030
Highest regularization parameter α highest_alpha137000000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.856; Stabil: 0.894; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.677

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id3wyfA00
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_id3wyfB00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id3wyfC01
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_id3wyfC02
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_id3wyfD00
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_id3wyfE00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

8. Citations (1)

9. Files and Curves (10)