+Open data
-Basic information
Entry | Database: PDB / ID: 5oid | ||||||
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Title | Complex Trichoplax STIL-NTD:human CEP85 coiled coil domain 4 | ||||||
Components |
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Keywords | PROTEIN BINDING / Centrosomes / centriole / STIL / CEP85 | ||||||
Function / homology | Function and homology information regulation of mitotic centrosome separation / protein localization to centrosome / smoothened signaling pathway / pericentriolar material / centrosome duplication / centriole / mitotic spindle organization / chromosome segregation / negative regulation of protein kinase activity / spindle pole ...regulation of mitotic centrosome separation / protein localization to centrosome / smoothened signaling pathway / pericentriolar material / centrosome duplication / centriole / mitotic spindle organization / chromosome segregation / negative regulation of protein kinase activity / spindle pole / centrosome / nucleolus / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | Trichoplax adhaerens (invertebrata) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.6 Å | ||||||
Authors | van Breugel, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Direct binding of CEP85 to STIL ensures robust PLK4 activation and efficient centriole assembly. Authors: Liu, Y. / Gupta, G.D. / Barnabas, D.D. / Agircan, F.G. / Mehmood, S. / Wu, D. / Coyaud, E. / Johnson, C.M. / McLaughlin, S.H. / Andreeva, A. / Freund, S.M.V. / Robinson, C.V. / Cheung, S.W.T. ...Authors: Liu, Y. / Gupta, G.D. / Barnabas, D.D. / Agircan, F.G. / Mehmood, S. / Wu, D. / Coyaud, E. / Johnson, C.M. / McLaughlin, S.H. / Andreeva, A. / Freund, S.M.V. / Robinson, C.V. / Cheung, S.W.T. / Raught, B. / Pelletier, L. / van Breugel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oid.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oid.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 5oid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/5oid ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oid | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40661.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Gene: TRIADDRAFT_58880 / Production host: Escherichia coli (E. coli) / Variant (production host): C41 / References: UniProt: B3S3X5 |
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#2: Protein | Mass: 10347.432 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEP85, CCDC21 / Production host: Escherichia coli (E. coli) / Variant (production host): C41 / References: UniProt: Q6P2H3 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES, pH 6.0 1.45 M MgSO4 2 mM DTT |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93927 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93927 Å / Relative weight: 1 |
Reflection | Resolution: 4.6→95 Å / Num. obs: 9532 / % possible obs: 100 % / Redundancy: 39.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.272 / Rpim(I) all: 0.043 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 4.6→5.14 Å / Redundancy: 42.1 % / Rmerge(I) obs: 3.033 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2642 / CC1/2: 0.397 / Rpim(I) all: 0.47 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 4.6→95 Å / SU ML: 1.13 / Cross valid method: FREE R-VALUE / σ(F): 0.45 / Phase error: 48.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.6→95 Å
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Refine LS restraints |
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LS refinement shell |
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