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5owu

Kap95:Nup1 complex

Method: X-RAY DIFFRACTION Dmax: 94.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Importin subunit beta-1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q06142

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 1–861 Not recorded Nucleoporin NUP1 × 1 （P20676） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；5 mg/ml protein in 5 mM Tris-HCl, pH 7.4 equilibrated against 90 mM (NH4)2SO4, 50 mM Na Cacodylate, pH 6.5, 13% PEG 8000 Resolution 2.00 Å R-free 0.219

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 5OWU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2BKU Kap95p:RanGTP complex Deposited 2005-02-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–861（861 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.279
2BKU Kap95p:RanGTP complex Deposited 2005-02-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–861（861 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.279
3EA5 Kap95p Binding Induces the Switch Loops of RanGDP to adopt the GTP-bound Conformation: Implications for Nuclear Import Complex Assembly Dynamics Deposited 2008-08-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–861（861 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；17% PEG 4000 0.1 M MES (pH 6.1) 10 mM MgCl2 125 mM NaCl 12% MPD 5 mg/ml GDP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.232
3EA5 Kap95p Binding Induces the Switch Loops of RanGDP to adopt the GTP-bound Conformation: Implications for Nuclear Import Complex Assembly Dynamics Deposited 2008-08-24 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–861（861 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；17% PEG 4000 0.1 M MES (pH 6.1) 10 mM MgCl2 125 mM NaCl 12% MPD 5 mg/ml GDP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.232
3ND2 Structure of Yeast Importin-beta (Kap95p) Deposited 2010-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–861（861 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20% PEG 4000, 0.1M MES pH 6.5, 20mM MgCl2, 125mM NaCl, 12% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.267

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IMB1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–861； UniProt 1–861

Nucleoporin NUP1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P20676

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 1–1076 Not recorded Importin subunit beta-1 × 1 （Q06142） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；5 mg/ml protein in 5 mM Tris-HCl, pH 7.4 equilibrated against 90 mM (NH4)2SO4, 50 mM Na Cacodylate, pH 6.5, 13% PEG 8000 Resolution 2.00 Å R-free 0.219

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 5OWU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4C31 Nup1:Sac3:Sus1 complex Deposited 2013-08-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 322–355（34 aa） Fragment：RESIDUES 322-355
Chain F 322–355（34 aa） Fragment：RESIDUES 322-355
Chain X 322–355（34 aa） Fragment：RESIDUES 322-355
Chain Y 322–355（34 aa） Fragment：RESIDUES 322-355
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；DESCRIBED IN DETAIL IN PUBLICATION, pH 6.0
Resolution 3.00 Å R-free 0.243
4MBE Sac3:Sus1:Cdc31:Nup1 complex Deposited 2013-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain G 316–340（25 aa） Fragment：FXF 1 repeat containing region, residues 316-340
Chain X 316–340（25 aa） Fragment：FXF 1 repeat containing region, residues 316-340
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.61 Å R-free 0.236
4MBE Sac3:Sus1:Cdc31:Nup1 complex Deposited 2013-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 316–340（25 aa） Fragment：FXF 1 repeat containing region, residues 316-340
Chain Y 316–340（25 aa） Fragment：FXF 1 repeat containing region, residues 316-340
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.61 Å R-free 0.236

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

View Construct and Data Evidence
UniProt name NUP1_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–1076； UniProt 1–1076

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 5owu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5owu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5owu
Deposition date deposition_date2017-09-04
Structure title titleKap95:Nup1 complex
Keywords keywordsnuclear transport, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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_guinier33.24 Å
Radius of gyration Rg (electron density) rg_electron32.19 Å
Forward intensity I(0) i0150875000.00
Molecular weight molecular_weight97640.0 kDa
Excluded volume excluded_volume122300 ų
Envelope volume envelope_volume167090 ų
Hydration-shell volume shell_volume42744 ų
Envelope diameter envelope_diameter95.2 Å
Shell Rg shell_rg40.11 Å
Envelope Rg envelope_rg30.72 Å
Shape Rg shape_rg32.19 Å
Total Rg total_rg32.88 Å
Total atoms total_atoms13657
Residues n_residues889
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 dmax94.8 Å
Rg (real space) rg_real32.91 Å
Rg uncertainty (real space) rg_real_error0.60 Å
I(0) (real space) i0_real1.5090e+08
I(0) uncertainty (real space) i0_real_error2.1370e+06
Rg (reciprocal space) rg_reciprocal33.06 Å
I(0) (reciprocal space) i0_reciprocal150900000.0000
Solution quality estimate total_estimate0.9088
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.4 Å
Skewness Skewness skewness-0.106
Kurtosis Kurtosis kurtosis-0.715
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19150000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.933
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd5owua_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.1 — Armadillo repeat

CATH v4.4 (1 domains)

Domain ID domain_id5owuA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
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8. Citations (1)

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9. Files and Curves (10)