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Yorodumi- PDB-5lsj: CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lsj | ||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN KINETOCHORE MIS12-CENP-C delta-HEAD2 COMPLEX | ||||||
Components |
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Keywords | CELL CYCLE / ALPHA-HELICAL | ||||||
Function / homology | Function and homology information MIS12/MIND type complex / skeletal muscle satellite cell proliferation / leucine zipper domain binding / spindle attachment to meiosis I kinetochore / inner kinetochore / attachment of spindle microtubules to kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region ...MIS12/MIND type complex / skeletal muscle satellite cell proliferation / leucine zipper domain binding / spindle attachment to meiosis I kinetochore / inner kinetochore / attachment of spindle microtubules to kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / kinetochore / fibrillar center / spindle pole / Separation of Sister Chromatids / azurophil granule lumen / mitotic cell cycle / midbody / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / nuclear body / nuclear speck / cell division / intracellular membrane-bounded organelle / Neutrophil degranulation / nucleolus / Golgi apparatus / DNA binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Vetter, I.R. / Petrovic, A. / Keller, J. / Liu, Y. | ||||||
Citation | Journal: Cell / Year: 2016 Title: Structure of the MIS12 Complex and Molecular Basis of Its Interaction with CENP-C at Human Kinetochores. Authors: Petrovic, A. / Keller, J. / Liu, Y. / Overlack, K. / John, J. / Dimitrova, Y.N. / Jenni, S. / van Gerwen, S. / Stege, P. / Wohlgemuth, S. / Rombaut, P. / Herzog, F. / Harrison, S.C. / ...Authors: Petrovic, A. / Keller, J. / Liu, Y. / Overlack, K. / John, J. / Dimitrova, Y.N. / Jenni, S. / van Gerwen, S. / Stege, P. / Wohlgemuth, S. / Rombaut, P. / Herzog, F. / Harrison, S.C. / Vetter, I.R. / Musacchio, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lsj.cif.gz | 248.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lsj.ent.gz | 199.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/5lsj ftp://data.pdbj.org/pub/pdb/validation_reports/ls/5lsj | HTTPS FTP |
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-Related structure data
Related structure data | 5lsiC 5lskSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24170.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MIS12 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q9H081 #2: Protein | Mass: 20522.359 Da / Num. of mol.: 2 / Fragment: UNP residues 31-205 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PMF1 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q6P1K2 #3: Protein | Mass: 20252.930 Da / Num. of mol.: 2 / Fragment: UNP residues 186-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DSN1, C20orf172, MIS13 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q9H410 #4: Protein | Mass: 13331.376 Da / Num. of mol.: 2 / Fragment: UNP residues 92-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NSL1, C1orf48, DC31, DC8, MIS14 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q96IY1 #5: Protein | Mass: 8501.529 Da / Num. of mol.: 2 / Fragment: UNP residues 1-71 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPC, CENPC1, ICEN7 / Plasmid: pST39 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q03188 |
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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: 2.9 Å3/Da / Density % sol: 57.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2M potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97857 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→45.5 Å / Num. obs: 31073 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 23.7 % / Biso Wilson estimate: 48.372 Å2 / Rmerge(I) obs: 0.351 / Net I/σ(I): 9.47 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LSK Resolution: 3.25→19.993 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 34.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.63 Å2 / Biso mean: 54.8084 Å2 / Biso min: 10.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→19.993 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
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