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Yorodumi- PDB-6ypc: Crystal structure of the kinetochore subunits H/I/K/T/W penta-com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ypc | |||||||||
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Title | Crystal structure of the kinetochore subunits H/I/K/T/W penta-complex from S. cerevisiae at 2.9 angstroms | |||||||||
Components | (Inner kinetochore subunit ...) x 5 | |||||||||
Keywords | CELL CYCLE / kinetochore / cenp complex / centromeres / chromosome segregation | |||||||||
Function / homology | Function and homology information negative regulation of kinetochore assembly / attachment of spindle microtubules to kinetochore / centromeric DNA binding / establishment of mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / DNA replication initiation / meiotic cell cycle / chromosome segregation / kinetochore / cell division ...negative regulation of kinetochore assembly / attachment of spindle microtubules to kinetochore / centromeric DNA binding / establishment of mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / DNA replication initiation / meiotic cell cycle / chromosome segregation / kinetochore / cell division / protein-containing complex binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Bellini, D. / Zhang, Z. / Barford, D. | |||||||||
Funding support | 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Crystal structure of the Cenp-HIKHead-TW sub-module of the inner kinetochore CCAN complex. Authors: Zhang, Z. / Bellini, D. / Barford, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ypc.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ypc.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ypc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ypc_validation.pdf.gz | 468 KB | Display | wwPDB validaton report |
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Full document | 6ypc_full_validation.pdf.gz | 480.8 KB | Display | |
Data in XML | 6ypc_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 6ypc_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/6ypc ftp://data.pdbj.org/pub/pdb/validation_reports/yp/6ypc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Inner kinetochore subunit ... , 5 types, 5 molecules KHTWI
#1: Protein | Mass: 12748.634 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: MCM22, YJR135C, J2122 / Production host: Escherichia coli (E. coli) / References: UniProt: P47167 |
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#2: Protein/peptide | Mass: 5153.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: MCM16, YPR046W / Production host: Escherichia coli (E. coli) / References: UniProt: Q12262 |
#3: Protein | Mass: 42154.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: CNN1, YFR046C / Production host: Escherichia coli (E. coli) / References: UniProt: P43618 |
#4: Protein | Mass: 10255.458 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: WIP1, YDR374W-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q2V2P8 |
#5: Protein | Mass: 28856.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: CTF3, CHL3, YLR381W / Production host: Escherichia coli (E. coli) / References: UniProt: Q12748 |
-Non-polymers , 1 types, 7 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.22 Å3/Da / Density % sol: 70.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1 M NaH2PO4 and 0.38M K2HPO4 with protein at 5.5 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9465 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9465 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→74.07 Å / Num. obs: 24344 / % possible obs: 100 % / Redundancy: 63.3 % / Biso Wilson estimate: 78.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.368 / Rpim(I) all: 0.047 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.9→3.07 Å / Num. unique obs: 3860 / CC1/2: 0.684 / Rpim(I) all: 1.826 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Z08 and 3B0D Resolution: 2.9→68.85 Å / SU ML: 0.4099 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.3898 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→68.85 Å
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Refine LS restraints |
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LS refinement shell |
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