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Yorodumi- PDB-4v8r: The crystal structures of the eukaryotic chaperonin CCT reveal it... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v8r | |||||||||
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Title | The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning | |||||||||
Components | (T-COMPLEX PROTEIN 1 SUBUNIT ...) x 8 | |||||||||
Keywords | CHAPERONE | |||||||||
Function / homology | Function and homology information Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / : / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / : / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding ...Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / : / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / : / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3.8 Å | |||||||||
Authors | Kalisman, N. / Schroder, G.F. / Levitt, M. | |||||||||
Citation | Journal: Embo J. / Year: 2011 Title: The Crystal Structure of Yeast Cct Reveals Intrinsic Asymmetry of Eukaryotic Cytosolic Chaperonins. Authors: Dekker, C. / Roe, S.M. / Mccormack, E.A. / Beuron, F. / Pearl, L.H. / Willison, K.R. | |||||||||
History |
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Remark 0 | THIS ENTRY 4AOL REFLECTS AN ALTERNATIVE SOLUTION OF THE ORIGINAL STRUCTURAL DATA (R3P9DSF) ...THIS ENTRY 4AOL REFLECTS AN ALTERNATIVE SOLUTION OF THE ORIGINAL STRUCTURAL DATA (R3P9DSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 3P9D: AUTHOR: C.DEKKER,S.M.ROE,E.A.MCCORMACK,F.BEURON,L.H.PEARL, K.R.WILLISON |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v8r.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v8r.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8r ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8r | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.24784, 0.92658, 0.2829), Vector: |
-Components
-T-COMPLEX PROTEIN 1 SUBUNIT ... , 8 types, 32 molecules AAAaBABaABAbBBBbADAdBDBdAEAeBEBeAGAgBGBgAHAhBHBhAQAqBQBqAZAzBZBz
#1: Protein | Mass: 60557.566 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P12612 #2: Protein | Mass: 57276.254 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39076 #3: Protein | Mass: 57740.449 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39078 #4: Protein | Mass: 61995.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40413 #5: Protein | Mass: 64939.828 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39077 #6: Protein | Mass: 59802.438 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P42943 #7: Protein | Mass: 61735.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P47079 #8: Protein | Mass: 59997.559 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39079 |
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-Non-polymers , 3 types, 96 molecules
#9: Chemical | ChemComp-ADP / #10: Chemical | ChemComp-BEF / #11: Chemical | ChemComp-MG / |
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-Details
Sequence details | THIS IS A HIS-CBP-STREP-TAG INSERTED BETWEEN PRO 374 AND LYS 375. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.32 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3P9D. |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 100 Å2 |
-Processing
Software | Name: CNS / Version: 1.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3.8→89.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 7525914.53 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 114.668 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 133.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.8→89.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.8→4.04 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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