← Back to search
5yu7

CRYSTAL STRUCTURE OF EXPORTIN-5

Method: X-RAY DIFFRACTION Dmax: 114.4 Å Quality: EXCELLENT
▼

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

Exportin-5

Homo sapiens

UniProt Q9HAV4

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 1–1204 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；283 K；PEG3350, Tacsimate, MPD, MgCl2, DTT Resolution 3.30 Å R-free 0.229

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.

Other PDB Difference from Current Entry 5YU7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3A6P Crystal structure of Exportin-5:RanGTP:pre-miRNA complex Deposited 2009-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1204（1204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.92 Å R-free 0.312
3A6P Crystal structure of Exportin-5:RanGTP:pre-miRNA complex Deposited 2009-09-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain F 1–1204（1204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.92 Å R-free 0.312
5YU6 CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX Deposited 2017-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1204（1204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DTT, MgCl2, spermine tetrahydrochloride
Resolution 3.00 Å R-free 0.269
5YU6 CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX Deposited 2017-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–1204（1204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DTT, MgCl2, spermine tetrahydrochloride
Resolution 3.00 Å R-free 0.269

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

View Construct and Data Evidence
UniProt name XPO5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1204； UniProt 1–1204

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 5yu7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5yu7
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5yu7
Deposition date deposition_date2017-11-20
Structure title titleCRYSTAL STRUCTURE OF EXPORTIN-5
Keywords keywordsRNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier36.51 Å
Radius of gyration Rg (electron density) rg_electron35.77 Å
Forward intensity I(0) i0240002000.00
Molecular weight molecular_weight127530.0 kDa
Excluded volume excluded_volume160940 ų
Envelope volume envelope_volume226470 ų
Hydration-shell volume shell_volume52026 ų
Envelope diameter envelope_diameter115.2 Å
Shell Rg shell_rg43.35 Å
Envelope Rg envelope_rg34.60 Å
Shape Rg shape_rg35.77 Å
Total Rg total_rg36.34 Å
Total atoms total_atoms8937
Residues n_residues1118
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax114.4 Å
Rg (real space) rg_real36.36 Å
Rg uncertainty (real space) rg_real_error0.93 Å
I(0) (real space) i0_real2.4000e+08
I(0) uncertainty (real space) i0_real_error4.1400e+06
Rg (reciprocal space) rg_reciprocal36.46 Å
I(0) (reciprocal space) i0_reciprocal240000000.0000
Solution quality estimate total_estimate0.9075
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary47.9 Å
Skewness Skewness skewness0.147
Kurtosis Kurtosis kurtosis-0.571
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha35880000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.957
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id5yu7A00
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)