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9d43

Cryo-EM structure of unliganded yeast Exportin Msn5

Method: ELECTRON MICROSCOPY Dmax: 115.2 Å Quality: EXCELLENT
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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–1224 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.39 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.

Other PDB Difference from Current Entry 9D43 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9D45 Cryo-EM structure of yeast Exportin Msn5 bound to cargo Pho4 and RanGTP Deposited 2024-08-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1224（1224 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9DXM Cryo-EM structure of yeast Exportin Msn5 bound to RanGTP and Pho4 (not modeled) (State 2-1) Deposited 2024-10-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1224（1224 aa）
Not recorded 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
9DZ6 Cryo-EM structure of yeast Exportin Msn5 bound to RanGTP and Pho4 (not modeled) (State 3-1) Deposited 2024-10-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1224（1224 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

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

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 9d43

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9d43
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9d43
Deposition date deposition_date2024-08-12
Structure title titleCryo-EM structure of unliganded yeast Exportin Msn5
Keywords keywordsKaryopherin, Exportin, Nuclear Export, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.74 Å
Radius of gyration Rg (electron density) rg_electron35.93 Å
Forward intensity I(0) i0271539000.00
Molecular weight molecular_weight138420.0 kDa
Excluded volume excluded_volume175490 ų
Envelope volume envelope_volume238480 ų
Hydration-shell volume shell_volume54479 ų
Envelope diameter envelope_diameter113.8 Å
Shell Rg shell_rg43.50 Å
Envelope Rg envelope_rg34.89 Å
Shape Rg shape_rg35.96 Å
Total Rg total_rg36.37 Å
Total atoms total_atoms9742
Residues n_residues1189
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax115.2 Å
Rg (real space) rg_real36.58 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real2.7150e+08
I(0) uncertainty (real space) i0_real_error4.5820e+06
Rg (reciprocal space) rg_reciprocal36.68 Å
I(0) (reciprocal space) i0_reciprocal271600000.0000
Solution quality estimate total_estimate0.9079
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.5 Å
Skewness Skewness skewness0.161
Kurtosis Kurtosis kurtosis-0.580
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha54220000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.970
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)