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5yu6

CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX

Method: X-RAY DIFFRACTION Dmax: 199.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Exportin-5

Homo sapiens

UniProt Q9HAV4

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–1204 Not recorded 13-mer peptide × 1 GTP-binding nuclear protein Ran × 1 （P62825） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DTT, MgCl2, spermine tetrahydrochloride Resolution 3.00 Å R-free 0.269
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 1–1204 Not recorded 13-mer peptide × 1 GTP-binding nuclear protein Ran × 1 （P62825） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DTT, MgCl2, spermine tetrahydrochloride Resolution 3.00 Å R-free 0.269

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 5YU6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3A6P Crystal structure of Exportin-5:RanGTP:pre-miRNA complex Deposited 2009-09-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–1204（1204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.92 Å R-free 0.312
3A6P Crystal structure of Exportin-5:RanGTP:pre-miRNA complex Deposited 2009-09-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain F 1–1204（1204 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.92 Å R-free 0.312
5YU7 CRYSTAL STRUCTURE OF EXPORTIN-5 Deposited 2017-11-20 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 1–1204（1204 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；PEG3350, Tacsimate, MPD, MgCl2, DTT
Resolution 3.30 Å R-free 0.229

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

View Construct and Data Evidence
UniProt name XPO5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1204； UniProt 1–1204 Author chain C； PDBConstruct 1–1204； UniProt 1–1204

GTP-binding nuclear protein Ran

Canis lupus familiaris

UniProt P62825

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–216 Not recorded Exportin-5 × 1 （Q9HAV4） 13-mer peptide × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DTT, MgCl2, spermine tetrahydrochloride Resolution 3.00 Å R-free 0.269
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 1–216 Not recorded Exportin-5 × 1 （Q9HAV4） 13-mer peptide × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DTT, MgCl2, spermine tetrahydrochloride Resolution 3.00 Å R-free 0.269

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 5YU6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BYU CANINE GDP-RAN Deposited 1998-10-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–216（216 aa） Fragment：ALL
Chain B 1–216（216 aa） Fragment：ALL
Not recorded MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.2
Resolution 2.15 Å R-free 0.243
1QG2 CANINE GDP-RAN R76E MUTANT Deposited 1999-04-20 Different construct Different mutation/modification 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 1–216（216 aa） Fragment：ALL
Mutation：R76E MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.20
Resolution 2.50 Å R-free 0.237
1QG4 CANINE GDP-RAN F72Y MUTANT Deposited 1999-04-20 Different construct Different mutation/modification 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 1–216（216 aa） Fragment：ALL
Mutation：F72Y MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.20
Resolution 2.50 Å R-free 0.237
1QG4 CANINE GDP-RAN F72Y MUTANT Deposited 1999-04-20 Different construct Different mutation/modification 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 1–216（216 aa） Fragment：ALL
Mutation：F72Y MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.20
Resolution 2.50 Å R-free 0.237
1WA5 Structure of the Cse1:Imp-alpha:RanGTP complex Deposited 2004-10-23 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–176（176 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；50mM TrisHCl, 200mM NaCl, 5mM Mg(OAc)2, .1mM GTP, 22% PEG3350 and 2% PEG400.
Resolution 2.00 Å R-free 0.216
2BKU Kap95p:RanGTP complex Deposited 2005-02-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–177（177 aa） Fragment：RESIDUES 1-177
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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–177（177 aa） Fragment：RESIDUES 1-177
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
3A6P Crystal structure of Exportin-5:RanGTP:pre-miRNA complex Deposited 2009-09-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–216（216 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.92 Å R-free 0.312
3A6P Crystal structure of Exportin-5:RanGTP:pre-miRNA complex Deposited 2009-09-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain H 1–216（216 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.92 Å R-free 0.312
3RAN CANINE GDP-RAN Q69L MUTANT Deposited 1998-10-19 Different mutation/modification 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 1–216（216 aa）
Mutation：Q69L MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.2
Resolution 2.15 Å R-free 0.243
3RAN CANINE GDP-RAN Q69L MUTANT Deposited 1998-10-19 Different mutation/modification 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 1–216（216 aa）
Mutation：Q69L MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.2
Resolution 2.15 Å R-free 0.243
3RAN CANINE GDP-RAN Q69L MUTANT Deposited 1998-10-19 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–216（216 aa）
Mutation：Q69L MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.2
Resolution 2.15 Å R-free 0.243
3RAN CANINE GDP-RAN Q69L MUTANT Deposited 1998-10-19 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–216（216 aa）
Mutation：Q69L MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；SEE PUBLICATION, pH 7.2
Resolution 2.15 Å R-free 0.243
3W3Z Crystal structure of Kap121p bound to RanGTP Deposited 2012-12-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–176（176 aa） Fragment：UNP residues 1-176
Not recorded MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 0.2M CaCl2, 10% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.298
5BXQ Structure of the NTF2:RanGDP complex Deposited 2015-06-09 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 C 1–216（216 aa）
Chain D 1–216（216 aa）
Chain E 1–216（216 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Li2SO4, 50 mM Na Citrate pH5.6, 15% PEG4000
Resolution 2.50 Å R-free 0.225

9 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAN_CANLF
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B； PDBConstruct 1–216； UniProt 1–216 Author chain D； PDBConstruct 1–216； UniProt 1–216

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 5yu6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5yu6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5yu6
Deposition date deposition_date2017-11-20
Structure title titleCRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX
Keywords keywordsRNA BINDING PROTEIN-NUCLEAR PROTEIN COMPLEX; RNA BINDING PROTEIN/NUCLEAR 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_guinier59.93 Å
Radius of gyration Rg (electron density) rg_electron60.66 Å
Forward intensity I(0) i01126330000.00
Molecular weight molecular_weight286540.0 kDa
Excluded volume excluded_volume361310 ų
Envelope volume envelope_volume531750 ų
Hydration-shell volume shell_volume79446 ų
Envelope diameter envelope_diameter223.1 Å
Shell Rg shell_rg53.83 Å
Envelope Rg envelope_rg59.71 Å
Shape Rg shape_rg60.63 Å
Total Rg total_rg60.55 Å
Total atoms total_atoms20096
Residues n_residues2508
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 dmax199.1 Å
Rg (real space) rg_real60.68 Å
Rg uncertainty (real space) rg_real_error2.01 Å
I(0) (real space) i0_real1.1260e+09
I(0) uncertainty (real space) i0_real_error2.3880e+07
Rg (reciprocal space) rg_reciprocal59.25 Å
I(0) (reciprocal space) i0_reciprocal1124000000.0000
Solution quality estimate total_estimate0.5683
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary53.6 Å
Skewness Skewness skewness0.565
Kurtosis Kurtosis kurtosis-0.395
Angular range angular_range— – 0.1300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha72800000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 0.962; Smooth: 0.073
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5yu6A00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id5yu6B00
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_id5yu6C00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id5yu6D00
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)