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Yorodumi- PDB-5h2x: Crystal structure of the karyopherin Kap60p bound to the SUMO pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h2x | ||||||
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Title | Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-172) | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/HYDROGENASE / nuclear import / PROTEIN TRANSPORT-HYDROGENASE 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Hirano, H. / Matsuura, Y. | ||||||
Funding support | Japan, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h2x.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h2x.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h2x_validation.pdf.gz | 426.8 KB | Display | wwPDB validaton report |
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Full document | 5h2x_full_validation.pdf.gz | 430 KB | Display | |
Data in XML | 5h2x_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 5h2x_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/5h2x ftp://data.pdbj.org/pub/pdb/validation_reports/h2/5h2x | HTTPS FTP |
-Related structure data
Related structure data | 5h2vC 5h2wSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46847.535 Da / Num. of mol.: 1 / 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 |
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#2: Protein/peptide | Mass: 2809.191 Da / Num. of mol.: 1 / Fragment: UNP residues 150-172 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 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % 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: 6.5 / Details: 0.1M sodium phosphate, 12% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 14, 2015 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.2→49.27 Å / Num. obs: 25386 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 25.26 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.065 / Rrim(I) all: 0.16 / Net I/σ(I): 9.9 / Num. measured all: 149220 / Scaling rejects: 69 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H2W Resolution: 2.2→49.268 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.15 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.79 Å2 / Biso mean: 32.3559 Å2 / Biso min: 13.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→49.268 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %
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