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4zj7

Crystal structure of the karyopherin Kap121p bound to the extreme C-terminus of the protein phosphatase Cdc14p

Method: X-RAY DIFFRACTION Dmax: 119.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Importin subunit beta-3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 Mutation：residues 80-90 deleted Tyrosine-protein phosphatase CDC14 × 1 （Q00684） 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

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 4ZJ7 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 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 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 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 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 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 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
3W3Z Crystal structure of Kap121p bound to RanGTP 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）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
5H2V Crystal structure of the karyopherin Kap121p bound to the SUMO protease Ulp1p Deposited 2016-10-18 Different mutation/modification 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 1–1078； UniProt 1–1089

Tyrosine-protein phosphatase CDC14

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q00684

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 517–551 Fragment：UNP residues 517-551 Importin subunit beta-3 × 1 （P32337） 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

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 4ZJ7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5XW4 Crystal structure of budding yeast Cdc14p (wild type) in the apo state Deposited 2017-06-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–374（374 aa） Fragment：UNP residues 1-374
Chain B 1–374（374 aa） Fragment：UNP residues 1-374
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Bis-Tris, ammonium sulfate, PEG4000
Resolution 1.85 Å R-free 0.203
5XW5 Crystal structure of budding yeast Cdc14p (C283S) bound to a Swi6p phosphopeptide Deposited 2017-06-29 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–374（374 aa） Fragment：UNP residues 1-374
Mutation：C283S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Bis-Tris, ammonium sulfate, PEG 4000
Resolution 1.85 Å R-free 0.217
5XW5 Crystal structure of budding yeast Cdc14p (C283S) bound to a Swi6p phosphopeptide Deposited 2017-06-29 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 1–374（374 aa） Fragment：UNP residues 1-374
Mutation：C283S SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Bis-Tris, ammonium sulfate, PEG 4000
Resolution 1.85 Å R-free 0.217
6G84 Structure of Cdc14 bound to CBK1 PxL motif Deposited 2018-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded CA CALCIUM ION × 4 EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；11% PEG3350, 0.2M Calcium Acetate
Resolution 2.47 Å R-free 0.270
6G85 Structure of Cdc14 bound to CBK1 PxL motif Deposited 2018-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；1.5% PEG 6000 and 0.1 M MES pH 6.0
Resolution 1.53 Å R-free 0.209
6G86 Structure of Cdc14 bound to SIC1 PxL motif Deposited 2018-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 P6G HEXAETHYLENE GLYCOL × 3 PEG DI(HYDROXYETHYL)ETHER × 5 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH6, 18% PEG200, 5% PEG 3000
Resolution 1.74 Å R-free 0.199

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDC14_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–35； UniProt 517–551

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 4zj7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4zj7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4zj7
Deposition date deposition_date2015-04-29
Structure title titleCrystal structure of the karyopherin Kap121p bound to the extreme C-terminus of the protein phosphatase Cdc14p
Keywords keywordskaryopherin, PROTEIN TRANSPORT-HYDROLASE complex; PROTEIN TRANSPORT/HYDROLASE
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_guinier36.03 Å
Radius of gyration Rg (electron density) rg_electron35.51 Å
Forward intensity I(0) i0177939000.00
Molecular weight molecular_weight110860.0 kDa
Excluded volume excluded_volume140460 ų
Envelope volume envelope_volume196910 ų
Hydration-shell volume shell_volume46983 ų
Envelope diameter envelope_diameter128.8 Å
Shell Rg shell_rg41.76 Å
Envelope Rg envelope_rg34.16 Å
Shape Rg shape_rg35.52 Å
Total Rg total_rg35.96 Å
Total atoms total_atoms7808
Residues n_residues1022
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 dmax119.0 Å
Rg (real space) rg_real35.87 Å
Rg uncertainty (real space) rg_real_error1.00 Å
I(0) (real space) i0_real1.7790e+08
I(0) uncertainty (real space) i0_real_error3.2280e+06
Rg (reciprocal space) rg_reciprocal35.97 Å
I(0) (reciprocal space) i0_reciprocal178000000.0000
Solution quality estimate total_estimate0.8774
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.7 Å
Skewness Skewness skewness0.126
Kurtosis Kurtosis kurtosis-0.339
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16120000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.966
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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

CATH v4.4 (2 domains)

Domain ID domain_id4zj7A01
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_id4zj7A02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1700 —
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8. Citations (1)

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9. Files and Curves (10)