[English] 日本語
Yorodumi- PDB-5h2w: Crystal structure of the karyopherin Kap60p bound to the SUMO pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h2w | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340) | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT/HYDROLASE / nuclear import / PROTEIN TRANSPORT-HYDROLASE complex | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Hirano, H. / Matsuura, Y. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: J. Mol. Biol. / Year: 2017 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5h2w.cif.gz | 180.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5h2w.ent.gz | 139.2 KB | Display | PDB format |
PDBx/mmJSON format | 5h2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/5h2w ftp://data.pdbj.org/pub/pdb/validation_reports/h2/5h2w | HTTPS FTP |
---|
-Related structure data
Related structure data | 5h2vC 5h2xC 2c1tS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SRP1, KAP60, YNL189W, N1606 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02821 #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.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ULP1, YPL020C, LPB11C / Production host: Escherichia coli (E. coli) / References: UniProt: Q02724, Ulp1 peptidase #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.1 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
---|---|
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 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å | ||||||||||||||||||
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 |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|