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Yorodumi- PDB-5lsi: CRYSTAL STRUCTURE OF THE KINETOCHORE MIS12 COMPLEX HEAD2 SUBDOMAI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lsi | ||||||
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Title | CRYSTAL STRUCTURE OF THE KINETOCHORE MIS12 COMPLEX HEAD2 SUBDOMAIN CONTAINING DSN1 AND NSL1 FRAGMENTS | ||||||
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 / attachment of spindle microtubules to kinetochore / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / fibrillar center ...MIS12/MIND type complex / skeletal muscle satellite cell proliferation / attachment of spindle microtubules to kinetochore / mitotic sister chromatid segregation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / fibrillar center / kinetochore / spindle pole / Separation of Sister Chromatids / azurophil granule lumen / nuclear body / nuclear speck / cell division / Neutrophil degranulation / nucleolus / extracellular region / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 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 | 5lsi.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lsi.ent.gz | 31.1 KB | Display | PDB format |
PDBx/mmJSON format | 5lsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/5lsi ftp://data.pdbj.org/pub/pdb/validation_reports/ls/5lsi | HTTPS FTP |
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-Related structure data
Related structure data | 5lsjC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15313.180 Da / Num. of mol.: 1 / Fragment: head2 domain, UNP residues 68-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DSN1, C20orf172, MIS13 / Plasmid: pGEX-2rbs / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q9H410 |
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#2: Protein | Mass: 8487.469 Da / Num. of mol.: 1 / Fragment: UNP residues 29-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NSL1, C1orf48, DC31, DC8, MIS14 / Plasmid: pGEX-2rbs / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon-plus-RIL / References: UniProt: Q96IY1 |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.4 Å3/Da / Density % sol: 48.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.6 Details: 2M ammonium sulfate, 0.2M potassium sodium phosphate, 0.1M sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 2, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→43.754 Å / Num. obs: 11845 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19.1 % / Biso Wilson estimate: 34.67 Å2 / Rmerge(I) obs: 0.242 / Net I/σ(I): 10.63 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LSK Resolution: 2.002→43.754 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.18 Å2 / Biso mean: 40.5025 Å2 / Biso min: 18.67 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.002→43.754 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: 4 / % reflection obs: 100 %
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