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6aho

Crystal structure of Kap114p

Method: X-RAY DIFFRACTION Dmax: 111.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Importin subunit beta-5

Saccharomyces cerevisiae

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–1004 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；0.43 M citric acid, 0.057 M BIS TRIS propane (pH 5.8), 17% PEG3350, 0.01 M Ethylenediaminetetraacetic acid disodium salt dihydrate, and 3% v/v ethanol Resolution 2.50 Å R-free 0.263

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 6AHO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8F0X Cryo-EM structure of Kap114 bound to H2A-H2B Deposited 2022-11-04 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1004（1004 aa）
Not recorded No recorded non-water small molecule 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 3.21 Å
8F19 Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) Deposited 2022-11-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1004（1004 aa）
Not recorded 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
8F1E Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) and H2A-H2B Deposited 2022-11-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1004（1004 aa）
Not recorded MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
8H5B The cryo-EM structure of nuclear transport receptor Kap114p complex with yeast TATA-box binding protein Deposited 2022-10-12 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1004（1004 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.03 Å

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 6–1009； UniProt 1–1004

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 6aho

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6aho
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6aho
Deposition date deposition_date2018-08-20
Structure title titleCrystal structure of Kap114p
Keywords keywordsKaryopherin, TATA box binding protein, Transcription, Nuclear transport, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.22 Å
Radius of gyration Rg (electron density) rg_electron38.50 Å
Forward intensity I(0) i0150966000.00
Molecular weight molecular_weight103680.0 kDa
Excluded volume excluded_volume131690 ų
Envelope volume envelope_volume196460 ų
Hydration-shell volume shell_volume42178 ų
Envelope diameter envelope_diameter112.3 Å
Shell Rg shell_rg45.86 Å
Envelope Rg envelope_rg36.34 Å
Shape Rg shape_rg38.49 Å
Total Rg total_rg39.04 Å
Total atoms total_atoms7294
Residues n_residues916
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 dmax111.8 Å
Rg (real space) rg_real39.40 Å
Rg uncertainty (real space) rg_real_error0.24 Å
I(0) (real space) i0_real1.4830e+08
I(0) uncertainty (real space) i0_real_error1.8150e+06
Rg (reciprocal space) rg_reciprocal39.15 Å
I(0) (reciprocal space) i0_reciprocal151000000.0000
Solution quality estimate total_estimate0.6815
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary61.5 Å
Skewness Skewness skewness-0.009
Kurtosis Kurtosis kurtosis-0.841
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha2.4930
Highest regularization parameter α highest_alpha18090000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.959; Stabil: 0.924; Sysdev: 0.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.248
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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)