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Yorodumi- PDB-6oqa: Crystal structure of CEP250 bound to FKBP12 in the presence of FK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oqa | ||||||
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Title | Crystal structure of CEP250 bound to FKBP12 in the presence of FK506-like novel natural product | ||||||
Components |
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Keywords | CELL CYCLE / ISOMERASE / FKBP12 / CEP250 / natural product / ternary complex | ||||||
Function / homology | Function and homology information centriole-centriole cohesion / detection of light stimulus involved in visual perception / protein localization to organelle / regulation of centriole-centriole cohesion / : / macrolide binding / activin receptor binding / cytoplasmic side of membrane / positive regulation of protein localization to centrosome / transforming growth factor beta receptor binding ...centriole-centriole cohesion / detection of light stimulus involved in visual perception / protein localization to organelle / regulation of centriole-centriole cohesion / : / macrolide binding / activin receptor binding / cytoplasmic side of membrane / positive regulation of protein localization to centrosome / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / signaling receptor inhibitor activity / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / non-motile cilium assembly / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / regulation of amyloid precursor protein catabolic process / microtubule organizing center / protein maturation by protein folding / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / cilium assembly / photoreceptor outer segment / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / sarcoplasmic reticulum membrane / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / photoreceptor inner segment / centriole / T cell activation / AURKA Activation by TPX2 / ciliary basal body / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / negative regulation of transforming growth factor beta receptor signaling pathway / protein localization / Z disc / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / Regulation of PLK1 Activity at G2/M Transition / protein folding / mitotic cell cycle / positive regulation of protein binding / protein refolding / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transmembrane transporter binding / amyloid fibril formation / protein domain specific binding / centrosome / protein kinase binding / perinuclear region of cytoplasm / protein-containing complex / extracellular exosome / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Lee, S.-J. / Shigdel, U.K. / Townson, S.A. / Verdine, G.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface. Authors: Shigdel, U.K. / Lee, S.J. / Sowa, M.E. / Bowman, B.R. / Robison, K. / Zhou, M. / Pua, K.H. / Stiles, D.T. / Blodgett, J.A.V. / Udwary, D.W. / Rajczewski, A.T. / Mann, A.S. / Mostafavi, S. / ...Authors: Shigdel, U.K. / Lee, S.J. / Sowa, M.E. / Bowman, B.R. / Robison, K. / Zhou, M. / Pua, K.H. / Stiles, D.T. / Blodgett, J.A.V. / Udwary, D.W. / Rajczewski, A.T. / Mann, A.S. / Mostafavi, S. / Hardy, T. / Arya, S. / Weng, Z. / Stewart, M. / Kenyon, K. / Morgenstern, J.P. / Pan, E. / Gray, D.C. / Pollock, R.M. / Fry, A.M. / Klausner, R.D. / Townson, S.A. / Verdine, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oqa.cif.gz | 187.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oqa.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 6oqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/6oqa ftp://data.pdbj.org/pub/pdb/validation_reports/oq/6oqa | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
-Protein , 2 types, 8 molecules ABEFCDGH
#1: Protein | Mass: 11967.705 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62942, peptidylprolyl isomerase #2: Protein | Mass: 11429.831 Da / Num. of mol.: 4 / Fragment: UNP residues 2078-2175 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEP250, CEP2, CNAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BV73 |
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-Non-polymers , 9 types, 268 molecules
#3: Chemical | ChemComp-60Z / ( #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Chemical | ChemComp-PGE / #8: Chemical | ChemComp-PG4 / #9: Chemical | ChemComp-MG / | #10: Chemical | ChemComp-MLA / | #11: Water | ChemComp-HOH / | |
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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: 3.13 Å3/Da / Density % sol: 60.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES, pH 7.0, 0.2 M sodium malonate, 21% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2013 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→136.05 Å / Num. obs: 53422 / % possible obs: 99.5 % / Redundancy: 3.7 % / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.22→2.3 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 5345 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→136.05 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.519 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.21 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 157.52 Å2 / Biso mean: 48.317 Å2 / Biso min: 22.03 Å2
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Refinement step | Cycle: final / Resolution: 2.2→136.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.203→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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