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Yorodumi- PDB-3rip: Crystal Structure of human gamma-tubulin complex protein 4 (GCP4) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rip | ||||||
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Title | Crystal Structure of human gamma-tubulin complex protein 4 (GCP4) | ||||||
Components | Gamma-tubulin complex component 4 | ||||||
Keywords | STRUCTURAL PROTEIN / helix bundles / gamma-tubulin ring complex / gamma-TuRC | ||||||
Function / homology | Function and homology information equatorial microtubule organizing center / gamma-tubulin ring complex / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / meiotic cell cycle ...equatorial microtubule organizing center / gamma-tubulin ring complex / gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / meiotic cell cycle / structural constituent of cytoskeleton / recycling endosome / spindle pole / microtubule cytoskeleton / mitotic cell cycle / protein-containing complex assembly / microtubule / centrosome / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Gregory-Pauron, L. / Guillet, V. / Mourey, L. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: Crystal structure of gamma-tubulin complex protein GCP4 provides insight into microtubule nucleation. Authors: Guillet, V. / Knibiehler, M. / Gregory-Pauron, L. / Remy, M.H. / Chemin, C. / Raynaud-Messina, B. / Bon, C. / Kollman, J.M. / Agard, D.A. / Merdes, A. / Mourey, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rip.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rip.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 3rip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/3rip ftp://data.pdbj.org/pub/pdb/validation_reports/ri/3rip | 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
#1: Protein | Mass: 77497.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TUBGCP4, 76P, GCP4 / Plasmid: pET26b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9UGJ1 | ||||
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#2: Chemical | ChemComp-MRD / ( | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IN THE SEQRES RECORDS CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.56 Å3/Da / Density % sol: 77.87 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 8-10% MPD (2-methyl-2,4-pentanediol), 0-20% glycerol (w/v), 300-400 mM Tris-Hcl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.033 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 77508 / Num. obs: 73248 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % |
Reflection shell | Resolution: 2.3→2.4 Å / Mean I/σ(I) obs: 2.45 / Num. unique all: 9151 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THE STARTING MODEL WAS SOLVED AND PARTIALLY REFINED FROM SAD DATA COLLECTED USING THE SELENEMETHIONINE PROTEIN Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.089 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.981 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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