3vyc

Crystal structure of unliganded Saccharomyces cerevisiae CRM1 (Xpo1p)

Method: X-RAY DIFFRACTION Dmax: 111.5 Å Quality: EXCELLENT

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

Exportin-1

Saccharomyces cerevisiae

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–1084 Mutation:a deletion mutant in which residues 377-413 and 971-984 are deleted No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.6;293 K;0.2M KF, 16% PEG3350, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.217

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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1033; 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 3vyc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3vyc
Deposition date deposition_date2012-09-22
Structure title titleCrystal structure of unliganded Saccharomyces cerevisiae CRM1 (Xpo1p)
Keywords keywordsHEAT repeat, nuclear export, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.43
Radius of gyration Rg (electron density) rg_electron35.72
Forward intensity I(0) i0176472000.00
Molecular weight molecular_weight110860.0 kDa
Excluded volume excluded_volume140580 ų
Envelope volume envelope_volume194960 ų
Hydration-shell volume shell_volume45257 ų
Envelope diameter envelope_diameter110.3
Shell Rg shell_rg42.94
Envelope Rg envelope_rg34.16
Shape Rg shape_rg35.71
Total Rg total_rg36.28
Total atoms total_atoms7802
Residues n_residues974
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 dmax111.5
Rg (real space) rg_real36.26
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real1.7650e+08
I(0) uncertainty (real space) i0_real_error2.4810e+06
Rg (reciprocal space) rg_reciprocal36.37
I(0) (reciprocal space) i0_reciprocal176500000.0000
Solution quality estimate total_estimate0.9086
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary51.9
Skewness Skewness skewness0.043
Kurtosis Kurtosis kurtosis-0.743
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22200000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.912

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3vyca_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.0 — automated matches

8. Citations (1)

9. Files and Curves (10)