+Open data
-Basic information
Entry | Database: PDB / ID: 4wau | ||||||
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Title | Crystal structure of CENP-M solved by native-SAD phasing | ||||||
Components | Centromere protein MCENPM | ||||||
Keywords | CELL CYCLE / native-SAD / S-SAD / sulfur-SAD / sulfur SAD / Mitosis / Kinetochore / CCAN / G-protein | ||||||
Function / homology | Function and homology information inner kinetochore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 / Separation of Sister Chromatids / nucleoplasm ...inner kinetochore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 / Separation of Sister Chromatids / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Weinert, T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Wang, M. | ||||||
Citation | Journal: Nat.Methods / Year: 2015 Title: Fast native-SAD phasing for routine macromolecular structure determination. Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wau.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wau.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/4wau ftp://data.pdbj.org/pub/pdb/validation_reports/wa/4wau | HTTPS FTP |
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-Related structure data
Related structure data | 4pgoC 4piiC 4r8tC 4r8uC 4tn8C 4tnoC 4wabC 4wbqC 4wbxC 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: 19245.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: residue 62 can not be observed in the density, however the density for the whole loop region is not very good. Source: (gene. exp.) Homo sapiens (human) / Gene: CENPM, C22orf18, ICEN39, PANE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSP4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.34 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM bicine pH 8.5, 11 % MPD, 8 mM spermidine / PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.0664 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.0664 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 40969 / % possible obs: 98.1 % / Redundancy: 140.4 % / Net I/σ(I): 92.37 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 32.3 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 16.94 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→45.28 Å / Cross valid method: FREE R-VALUE / σ(F): 1.7 / Phase error: 14.5 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→45.28 Å
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Refine LS restraints |
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LS refinement shell |
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