+Open data
-Basic information
Entry | Database: PDB / ID: 8ibh | ||||||
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Title | Cep57 C-terminal domain | ||||||
Components | Centrosomal protein of 57 kDa | ||||||
Keywords | CELL CYCLE / coiled-coil / cell centrosome / scaffold | ||||||
Function / homology | Function and homology information ciliary basal body-plasma membrane docking / microtubule anchoring / gamma-tubulin binding / fibroblast growth factor binding / spermatid development / fibroblast growth factor receptor signaling pathway / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes ...ciliary basal body-plasma membrane docking / microtubule anchoring / gamma-tubulin binding / fibroblast growth factor binding / spermatid development / fibroblast growth factor receptor signaling pathway / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of G2/M transition of mitotic cell cycle / AURKA Activation by TPX2 / protein homooligomerization / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / microtubule binding / microtubule / centrosome / Golgi apparatus / protein homodimerization activity / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Chen, T. / Yeh, H.-W. / Cheng, H.-C. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Cep57 regulates human centrosomes through multivalent interactions. Authors: Yeh, H.W. / Chen, P.P. / Yeh, T.C. / Lin, S.L. / Chen, Y.T. / Lin, W.P. / Chen, T. / Pang, J.M. / Lin, K.T. / Wang, L.H. / Lin, Y.C. / Shih, O. / Jeng, U.S. / Hsia, K.C. / Cheng, H.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ibh.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ibh.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ibh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ibh_validation.pdf.gz | 426.7 KB | Display | wwPDB validaton report |
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Full document | 8ibh_full_validation.pdf.gz | 427.6 KB | Display | |
Data in XML | 8ibh_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 8ibh_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/8ibh ftp://data.pdbj.org/pub/pdb/validation_reports/ib/8ibh | HTTPS FTP |
-Related structure data
Related structure data | 4l0rS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 12536.278 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEP57, KIAA0092, TSP57 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86XR8 |
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#2: 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: 1.86 Å3/Da / Density % sol: 33.81 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium chloride, 0.1 M HEPES pH 7.5, 1.6 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→30 Å / Num. obs: 7114 / % possible obs: 99.3 % / Redundancy: 9.2 % / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 38 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / Num. unique obs: 681 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L0R Resolution: 2.1→24.91 Å / SU ML: 0.2125 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5964 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→24.91 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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