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- PDB-5h2w: Crystal structure of the karyopherin Kap60p bound to the SUMO pro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h2w | ||||||
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Title | Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340) | ||||||
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![]() | PROTEIN TRANSPORT/HYDROLASE / nuclear import / PROTEIN TRANSPORT-HYDROLASE complex | ||||||
Function / homology | ![]() Ulp1 peptidase / proteasome localization / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / import into nucleus / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear import signal receptor activity / nuclear localization sequence binding ...Ulp1 peptidase / proteasome localization / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / import into nucleus / NLS-dependent protein nuclear import complex / protein targeting to membrane / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / cysteine-type peptidase activity / protein import into nucleus / G2/M transition of mitotic cell cycle / disordered domain specific binding / nuclear envelope / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hirano, H. / Matsuura, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the Karyopherins Kap121p and Kap60p Bound to the Nuclear Pore-Targeting Domain of the SUMO Protease Ulp1p Authors: Hirano, H. / Kobayashi, J. / Matsuura, Y. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.7 KB | Display | ![]() |
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PDB format | ![]() | 139.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 459.8 KB | Display | ![]() |
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Full document | ![]() | 466.7 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h2vC ![]() 5h2xC ![]() 2c1tS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46847.535 Da / Num. of mol.: 2 / Fragment: UNP residues 88-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SRP1, KAP60, YNL189W, N1606 / Production host: ![]() ![]() #2: Protein | Mass: 22122.736 Da / Num. of mol.: 2 / Fragment: UNP residues 150-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: ULP1, YPL020C, LPB11C / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.1 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M MES, 0.1M calcium acetate, 12% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2014 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.5→30.37 Å / Num. obs: 29881 / % possible obs: 90.5 % / Redundancy: 1.6 % / Biso Wilson estimate: 29.84 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Rrim(I) all: 0.07 / Net I/σ(I): 5.9 / Num. measured all: 47966 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2C1T Resolution: 2.5→27.028 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→27.028 Å
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Refine LS restraints |
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LS refinement shell |
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