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3w3z

Crystal structure of Kap121p bound to RanGTP

Method: X-RAY DIFFRACTION Dmax: 137.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Importin subunit beta-3

Saccharomyces cerevisiae

UniProt P32337

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 1–1089 Non-standard monomer：Yes (specific site not provided by mmCIF) GTP-binding nuclear protein Ran × 1 （P62825） 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

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 3W3Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3W3T Crystal structure of Kap121p Deposited 2012-12-28 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 1–1089（1089 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% 2-popanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.247
3W3U Crystal structure of Kap121p mutant R349A/Q350A/D353A/E396A/N430K/D438A/N477A Deposited 2012-12-28 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 1–1089（1089 aa）
Mutation：R349A, Q350A, D353A, E396A, N430K, D438A, N477A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% 2-propanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.267
3W3V Crystal structure of Kap121p mutant D353K/E396K/D438K Deposited 2012-12-28 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 1–1089（1089 aa）
Mutation：D353K, E396K, D438K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% 2-propanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.252
3W3W Crystal structure of Kap121p bound to Ste12p Deposited 2012-12-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1089（1089 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% 2-propanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.256
3W3X Crystal structure of Kap121p bound to Pho4p Deposited 2012-12-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1089（1089 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% 2-propanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.268
3W3Y Crystal structure of Kap121p bound to Nup53p Deposited 2012-12-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1089（1089 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% 2-propanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.297
4ZJ7 Crystal structure of the karyopherin Kap121p bound to the extreme C-terminus of the protein phosphatase Cdc14p Deposited 2015-04-29 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1089（1089 aa）
Mutation：residues 80-90 deleted No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 20000, 2-propanol
Resolution 2.40 Å R-free 0.252
5H2V Crystal structure of the karyopherin Kap121p bound to the SUMO protease Ulp1p Deposited 2016-10-18 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1089（1089 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% 2-propanol, 24% PEG20000
Resolution 2.80 Å R-free 0.241

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IMB3_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1089； UniProt 1–1089

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–176 Fragment：UNP residues 1-176 Importin subunit beta-3 × 1 （P32337） 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

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 3W3Z 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 oligomeric state 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 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 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 construct 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 construct 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 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）
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 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）
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 construct 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 construct 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
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
5YU6 CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX Deposited 2017-11-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–216（216 aa）
Not recorded 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
5YU6 CRYSTAL STRUCTURE OF EXPORTIN-5:RANGTP COMPLEX Deposited 2017-11-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–216（216 aa）
Not recorded 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

9 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAN_CANFA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–176； UniProt 1–176

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 3w3z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3w3z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3w3z
Deposition date deposition_date2012-12-28
Structure title titleCrystal structure of Kap121p bound to RanGTP
Keywords keywordsHEAT repeat, nuclear import, PROTEIN TRANSPORT-NUCLEAR PROTEIN complex; PROTEIN TRANSPORT/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_guinier40.48 Å
Radius of gyration Rg (electron density) rg_electron40.47 Å
Forward intensity I(0) i0248259000.00
Molecular weight molecular_weight130880.0 kDa
Excluded volume excluded_volume164700 ų
Envelope volume envelope_volume232330 ų
Hydration-shell volume shell_volume49144 ų
Envelope diameter envelope_diameter139.0 Å
Shell Rg shell_rg44.89 Å
Envelope Rg envelope_rg39.05 Å
Shape Rg shape_rg40.50 Å
Total Rg total_rg40.65 Å
Total atoms total_atoms9142
Residues n_residues1162
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 dmax137.2 Å
Rg (real space) rg_real40.55 Å
Rg uncertainty (real space) rg_real_error1.77 Å
I(0) (real space) i0_real2.4830e+08
I(0) uncertainty (real space) i0_real_error4.6860e+06
Rg (reciprocal space) rg_reciprocal40.48 Å
I(0) (reciprocal space) i0_reciprocal248200000.0000
Solution quality estimate total_estimate0.8815
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.7 Å
Skewness Skewness skewness0.324
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14450000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.918; Smooth: 0.858
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3w3zb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins

CATH v4.4 (1 domains)

Domain ID domain_id3w3zB00
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)