8f19

Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP)

Method: ELECTRON MICROSCOPY Dmax: 112.1 Å Quality: REASONABLE

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

Importin subunit beta-5

Saccharomyces cerevisiae S288C

UniProt P53067

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 1–1004 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 7.5;20 mM Tris pH 7.5, 300 mM NaCl, 2 mM MgCl2, 1 mM TCEP, and 0.1% NP-40 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.49 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.

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

View Construct and Data Evidence
UniProt name IMB5_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–1004; UniProt 1–1004

GTP-binding nuclear protein GSP1/CNR1

Saccharomyces cerevisiae S288C

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 1–179 Mutation:Q71L Importin subunit beta-5 × 1 (P53067) GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;20 mM Tris pH 7.5, 300 mM NaCl, 2 mM MgCl2, 1 mM TCEP, and 0.1% NP-40 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.49 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 1–179; UniProt 1–179

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 8f19

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8f19
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8f19
Deposition date deposition_date2022-11-04
Structure title titleCryo-EM structure of Kap114 bound to Gsp1 (RanGTP)
Keywords keywordsKaryopherin Beta, Nuclear Transport, GTPase, PROTEIN TRANSPORT-NUCLEAR PROTEIN complex; PROTEIN TRANSPORT/NUCLEAR PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier36.57
Radius of gyration Rg (electron density) rg_electron36.01
Forward intensity I(0) i0218927000.00
Molecular weight molecular_weight123890.0 kDa
Excluded volume excluded_volume157040 ų
Envelope volume envelope_volume210860 ų
Hydration-shell volume shell_volume48599 ų
Envelope diameter envelope_diameter112.1
Shell Rg shell_rg42.91
Envelope Rg envelope_rg35.15
Shape Rg shape_rg36.00
Total Rg total_rg36.56
Total atoms total_atoms8717
Residues n_residues1087
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 dmax112.1
Rg (real space) rg_real36.42
Rg uncertainty (real space) rg_real_error0.67
I(0) (real space) i0_real2.1890e+08
I(0) uncertainty (real space) i0_real_error3.4360e+06
Rg (reciprocal space) rg_reciprocal36.52
I(0) (reciprocal space) i0_reciprocal218900000.0000
Solution quality estimate total_estimate0.6461
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.9
Skewness Skewness skewness0.096
Kurtosis Kurtosis kurtosis-0.740
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44470000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)