9dxm

Cryo-EM structure of yeast Exportin Msn5 bound to RanGTP and Pho4 (not modeled) (State 2-1)

Method: ELECTRON MICROSCOPY Dmax: 119.0 Å Quality: GOOD

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

Protein MSN5

Saccharomyces cerevisiae

UniProt P52918

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–1224 Not recorded GTP-binding nuclear protein GSP1/CNR1 × 1 (P32835) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 Å

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MSN5_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1224; UniProt 1–1224

GTP-binding nuclear protein GSP1/CNR1

Saccharomyces cerevisiae

UniProt P32835

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 2–179 Mutation:Q71L Protein MSN5 × 1 (P52918) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.4 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.20 Å

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.

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

View Construct and Data Evidence
UniProt name GSP1_YEAST
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 3–180; UniProt 2–179

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 9dxm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dxm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9dxm
Deposition date deposition_date2024-10-11
Structure title titleCryo-EM structure of yeast Exportin Msn5 bound to RanGTP and Pho4 (not modeled) (State 2-1)
Keywords keywordsKaryopherin, Exportin, Nuclear Export, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier39.66
Radius of gyration Rg (electron density) rg_electron39.02
Forward intensity I(0) i0279053000.00
Molecular weight molecular_weight142770.0 kDa
Excluded volume excluded_volume181540 ų
Envelope volume envelope_volume249200 ų
Hydration-shell volume shell_volume53142 ų
Envelope diameter envelope_diameter121.9
Shell Rg shell_rg45.71
Envelope Rg envelope_rg37.25
Shape Rg shape_rg39.03
Total Rg total_rg39.38
Total atoms total_atoms20213
Residues n_residues1224
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 dmax119.0
Rg (real space) rg_real39.50
Rg uncertainty (real space) rg_real_error0.72
I(0) (real space) i0_real2.7910e+08
I(0) uncertainty (real space) i0_real_error4.7490e+06
Rg (reciprocal space) rg_reciprocal39.61
I(0) (reciprocal space) i0_reciprocal279100000.0000
Solution quality estimate total_estimate0.8865
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.6
Skewness Skewness skewness0.108
Kurtosis Kurtosis kurtosis-0.716
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30770000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.990; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.551

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)