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3nd2

Structure of Yeast Importin-beta (Kap95p)

Method: X-RAY DIFFRACTION Dmax: 91.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Importin subunit beta-1

Saccharomyces cerevisiae

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–861 Not recorded No other associated polymer 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

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 3ND2 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
5OWU Kap95:Nup1 complex Deposited 2017-09-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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；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

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

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 3nd2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3nd2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3nd2
Deposition date deposition_date2010-06-06
Structure title titleStructure of Yeast Importin-beta (Kap95p)
Keywords keywordsimportin, karyopherin, nuclear import, receptor, Nuclear 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_guinier32.52 Å
Radius of gyration Rg (electron density) rg_electron31.45 Å
Forward intensity I(0) i0142621000.00
Molecular weight molecular_weight94714.0 kDa
Excluded volume excluded_volume118710 ų
Envelope volume envelope_volume161650 ų
Hydration-shell volume shell_volume42451 ų
Envelope diameter envelope_diameter92.5 Å
Shell Rg shell_rg39.39 Å
Envelope Rg envelope_rg29.93 Å
Shape Rg shape_rg31.45 Å
Total Rg total_rg32.18 Å
Total atoms total_atoms6653
Residues n_residues861
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 dmax91.8 Å
Rg (real space) rg_real32.19 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real1.4260e+08
I(0) uncertainty (real space) i0_real_error2.0850e+06
Rg (reciprocal space) rg_reciprocal32.33 Å
I(0) (reciprocal space) i0_reciprocal142600000.0000
Solution quality estimate total_estimate0.9088
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.7 Å
Skewness Skewness skewness-0.128
Kurtosis Kurtosis kurtosis-0.690
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20650000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.944
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3nd2a_
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_id3nd2A00
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)