3wyg

Crystal structure of Xpo1p-PKI-Gsp1p-GTP complex

Method: X-RAY DIFFRACTION Dmax: 108.6 Å Quality: EXCELLENT

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 1–182 Fragment:UNP residues 1-182 Mutation:Q71L Exportin-1 × 1 (P30822) cAMP-dependent protein kinase inhibitor alpha × 1 (P61925) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.7;0.1M TRIS, 15% PEG20000, PH 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K Resolution 2.15 Å R-free 0.220

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 3 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 1–182; UniProt 1–182

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) cAMP-dependent protein kinase inhibitor alpha × 1 (P61925) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.7;0.1M TRIS, 15% PEG20000, PH 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K Resolution 2.15 Å R-free 0.220

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 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XPO1_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 3–1049; UniProt 1–1084

cAMP-dependent protein kinase inhibitor alpha

Homo sapiens

UniProt P61925

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 D; UniProt 1–76 Mutation:S35L Gsp1p × 1 (E7KFU1) Exportin-1 × 1 (P30822) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.7;0.1M TRIS, 15% PEG20000, PH 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K Resolution 2.15 Å R-free 0.220

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.

90 other PDB entries and 100 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IPKA_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–76; UniProt 1–76

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 3wyg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3wyg
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3wyg
Deposition date deposition_date2014-08-26
Structure title titleCrystal structure of Xpo1p-PKI-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_guinier35.02
Radius of gyration Rg (electron density) rg_electron34.19
Forward intensity I(0) i0266384000.00
Molecular weight molecular_weight136810.0 kDa
Excluded volume excluded_volume173410 ų
Envelope volume envelope_volume219690 ų
Hydration-shell volume shell_volume51954 ų
Envelope diameter envelope_diameter107.9
Shell Rg shell_rg42.60
Envelope Rg envelope_rg33.50
Shape Rg shape_rg34.19
Total Rg total_rg34.81
Total atoms total_atoms9636
Residues n_residues1193
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 dmax108.6
Rg (real space) rg_real34.85
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real2.6640e+08
I(0) uncertainty (real space) i0_real_error3.4130e+06
Rg (reciprocal space) rg_reciprocal34.96
I(0) (reciprocal space) i0_reciprocal266400000.0000
Solution quality estimate total_estimate0.9102
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary43.4
Skewness Skewness skewness0.099
Kurtosis Kurtosis kurtosis-0.640
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha45230000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.979

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3wyga_
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 (1 domains)

Domain ID domain_id3wygA00
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)