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3icq

Karyopherin nuclear state

Method: X-RAY DIFFRACTION Dmax: 179.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Exportin-T

Schizosaccharomyces pombe

UniProt O94258

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–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain T； UniProt 1–978 Not recorded GTP-binding nuclear protein GSP1/CNR1 × 1 （P32835） RNA (62-MER) × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；100mM Bis-Tris, pH5.5, 20% PEG3350, 180mM sodium acetate at 18 degrees, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.294
2 Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain U； UniProt 1–978 Not recorded GTP-binding nuclear protein GSP1/CNR1 × 1 （P32835） RNA (62-MER) × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；100mM Bis-Tris, pH5.5, 20% PEG3350, 180mM sodium acetate at 18 degrees, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.294

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 3ICQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3IBV Karyopherin cytosolic state Deposited 2009-07-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–978（978 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM MES, pH6.5, 30% PEG400, 160mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.313
3IBV Karyopherin cytosolic state Deposited 2009-07-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–978（978 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM MES, pH6.5, 30% PEG400, 160mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.10 Å R-free 0.313

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

View Construct and Data Evidence
UniProt name XPOT_SCHPO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain T； PDBConstruct 3–980； UniProt 1–978 Author chain U； PDBConstruct 3–980； UniProt 1–978

GTP-binding nuclear protein GSP1/CNR1

Saccharomyces cerevisiae

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–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain B； UniProt 9–179 Fragment：Ran, UNP residues 9-179 Mutation：Q71L Exportin-T × 1 （O94258） RNA (62-MER) × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；100mM Bis-Tris, pH5.5, 20% PEG3350, 180mM sodium acetate at 18 degrees, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.294
2 Protein–RNA Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain C； UniProt 9–179 Fragment：Ran, UNP residues 9-179 Mutation：Q71L Exportin-T × 1 （O94258） RNA (62-MER) × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；100mM Bis-Tris, pH5.5, 20% PEG3350, 180mM sodium acetate at 18 degrees, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 3.20 Å R-free 0.294

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 3ICQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2X19 Crystal structure of Importin13 - RanGTP complex Deposited 2009-12-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 8–179（172 aa） Fragment：RESIDUES 8-179
Mutation：YES GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；100MM BIS-TRIS PH 6 23% 9W/V) PEG 3350 100MM NA-THIIOCYANATE RT
Resolution 2.80 Å R-free 0.268
3M1I Crystal structure of yeast CRM1 (Xpo1p) in complex with yeast RanBP1 (Yrb1p) and yeast RanGTP (Gsp1pGTP) Deposited 2010-03-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–219（219 aa）
Mutation：Q71L GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；0.1M Bis-Tris, 0.2M ammonium nitrate, 18% PEG3350, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.220
8DYO Cryo-EM structure of Importin-4 bound to RanGTP Deposited 2022-08-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–219（219 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 7.10 Å
8F19 Cryo-EM structure of Kap114 bound to Gsp1 (RanGTP) Deposited 2022-11-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–179（179 aa）
Mutation：Q71L 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 construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–179（179 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
8F7A Cryo-EM structure of Importin-9 bound to RanGTP Deposited 2022-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–219（219 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 3.78 Å
8QYZ Crystal structure of hiNES2 in complex with Xpo1 and RanGTP Deposited 2023-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–182（182 aa）
Mutation：1-182, Q71L GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Tris, PEG 20K, magnesium acetate
Resolution 3.00 Å R-free 0.247
8QYZ Crystal structure of hiNES2 in complex with Xpo1 and RanGTP Deposited 2023-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–182（182 aa）
Mutation：1-182, Q71L GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Tris, PEG 20K, magnesium acetate
Resolution 3.00 Å R-free 0.247
8QYZ Crystal structure of hiNES2 in complex with Xpo1 and RanGTP Deposited 2023-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–182（182 aa）
Mutation：1-182, Q71L GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Tris, PEG 20K, magnesium acetate
Resolution 3.00 Å R-free 0.247
8QYZ Crystal structure of hiNES2 in complex with Xpo1 and RanGTP Deposited 2023-10-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–182（182 aa）
Mutation：1-182, Q71L GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Tris, PEG 20K, magnesium acetate
Resolution 3.00 Å R-free 0.247
9D45 Cryo-EM structure of yeast Exportin Msn5 bound to cargo Pho4 and RanGTP Deposited 2024-08-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–179（178 aa）
Mutation：Q71L 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 construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–179（178 aa）
Mutation：Q71L 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 construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–179（178 aa）
Mutation：Q71L 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
9OGB Cryo-EM structure of human exportin-1 conjugated with selinexor and bound to yeast RAN-GTP and human ASB8-ELOB/C Deposited 2025-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–179（179 aa） Fragment：residues 1-179
Mutation：Q71L V6A selinexor, bound form × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 110 mM KOAc, 2 mM Mg(OAc)2, 2 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å

11 other PDB entries and 14 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 1–171； UniProt 9–179 Author chain C； PDBConstruct 1–171； UniProt 9–179

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 3icq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3icq
Deposition date deposition_date2009-07-18
Structure title titleKaryopherin nuclear state
Keywords keywordskaryopherin, exportin, HEAT repeat, tRNA, GTPase, RNA BINDING PROTEIN; RNA BINDING 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_guinier52.93 Å
Radius of gyration Rg (electron density) rg_electron52.32 Å
Forward intensity I(0) i01273350000.00
Molecular weight molecular_weight273490.0 kDa
Excluded volume excluded_volume331070 ų
Envelope volume envelope_volume506210 ų
Hydration-shell volume shell_volume80101 ų
Envelope diameter envelope_diameter173.7 Å
Shell Rg shell_rg57.11 Å
Envelope Rg envelope_rg50.33 Å
Shape Rg shape_rg52.29 Å
Total Rg total_rg52.52 Å
Total atoms total_atoms19121
Residues n_residues2346
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 dmax179.1 Å
Rg (real space) rg_real52.99 Å
Rg uncertainty (real space) rg_real_error1.92 Å
I(0) (real space) i0_real1.2730e+09
I(0) uncertainty (real space) i0_real_error2.7420e+07
Rg (reciprocal space) rg_reciprocal52.85 Å
I(0) (reciprocal space) i0_reciprocal1273000000.0000
Solution quality estimate total_estimate0.8679
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.8 Å
Skewness Skewness skewness0.261
Kurtosis Kurtosis kurtosis-0.757
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha185900000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.870
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3icqB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3icqC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)