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Yorodumi- PDB-5u1t: Crystal structure of the Saccharomyces cerevisiae separase-securi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u1t | |||||||||
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Title | Crystal structure of the Saccharomyces cerevisiae separase-securin complex at 2.6 angstrom resolution | |||||||||
Components |
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Keywords | HYDROLASE / separase-securin complex / ESP1 / PDS1 / chromosome segregation / cohesion / helical region / inhibition / chaperon | |||||||||
Function / homology | Function and homology information positive regulation of metaphase/anaphase transition of meiotic cell cycle / Separation of Sister Chromatids / separase-securin complex / separase / negative regulation of protein localization to nucleolus / negative regulation of exit from mitosis / regulation of mitotic spindle elongation / meiotic chromosome separation / positive regulation of exit from mitosis / mitotic spindle pole body ...positive regulation of metaphase/anaphase transition of meiotic cell cycle / Separation of Sister Chromatids / separase-securin complex / separase / negative regulation of protein localization to nucleolus / negative regulation of exit from mitosis / regulation of mitotic spindle elongation / meiotic chromosome separation / positive regulation of exit from mitosis / mitotic spindle pole body / meiosis I / recombinational repair / negative regulation of phosphoprotein phosphatase activity / mitotic sister chromatid segregation / molecular function activator activity / protein localization / mitotic spindle / spindle / cell division / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / enzyme binding / mitochondrion / proteolysis / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Luo, S. / Tong, L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2017 Title: Molecular mechanism for the regulation of yeast separase by securin. Authors: Luo, S. / Tong, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u1t.cif.gz | 327.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u1t.ent.gz | 257.1 KB | Display | PDB format |
PDBx/mmJSON format | 5u1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/5u1t ftp://data.pdbj.org/pub/pdb/validation_reports/u1/5u1t | HTTPS FTP |
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-Related structure data
Related structure data | 5u1sSC 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: 184044.469 Da / Num. of mol.: 1 Fragment: UNP residues 71-1630, helical domain and catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: ESP1, YGR098C / Plasmid: pFL / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five Cell / References: UniProt: Q03018, separase |
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#2: Protein | Mass: 13366.599 Da / Num. of mol.: 1 Fragment: UNP residues 258-373, separase interaction segment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: PDS1, YDR113C, YD9727.08C / Plasmid: pFL / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five Cell / References: UniProt: P40316 |
#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: 3.15 Å3/Da / Density % sol: 60.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 0.25 M Na/K-phosphate (pH 6.0) and 14% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 18, 2016 / Details: DECTRIS PILATUS 6M-F | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. obs: 77491 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 62.34 Å2 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.059 / Rrim(I) all: 0.153 / Χ2: 1.06 / Net I/av σ(I): 14.42 / Net I/σ(I): 4.3 / Num. measured all: 774372 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U1S Resolution: 2.6→48.667 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.36 Å2 / Biso mean: 72.031 Å2 / Biso min: 35.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→48.667 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: 14
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