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Yorodumi- PDB-4v94: Molecular architecture of the eukaryotic chaperonin TRiC/CCT deri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v94 | |||||||||
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Title | Molecular architecture of the eukaryotic chaperonin TRiC/CCT derived by a combination of chemical crosslinking and mass-spectrometry, XL-MS | |||||||||
Components | (T-complex protein 1 subunit ...) x 8 | |||||||||
Keywords | CHAPERONE / chaperonin / nano cage / protein folding / molecular chaperone / ATPase / cytosol | |||||||||
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 / MANUALLY PLACED / Resolution: 3.8 Å | |||||||||
Authors | Leitner, A. / Joachimiak, L.A. / Bracher, A. / Walzthoeni, T. / Chen, B. / Monkemeyer, L. / Pechmann, S. / Holmes, S. / Cong, Y. / Ma, B. ...Leitner, A. / Joachimiak, L.A. / Bracher, A. / Walzthoeni, T. / Chen, B. / Monkemeyer, L. / Pechmann, S. / Holmes, S. / Cong, Y. / Ma, B. / Ludtke, S. / Chiu, W. / Hartl, F.U. / Aebersold, R. / Frydman, J. | |||||||||
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 | THE ENTRIES 4D8Q AND 4D8R REFLECT AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R3P9DSF AND ...THE ENTRIES 4D8Q AND 4D8R REFLECT AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R3P9DSF AND R3P9ESF ORIGINAL DATA DETERMINED BY 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 | 4v94.cif.gz | 4.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v94.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/4v94 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/4v94 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-T-complex protein 1 subunit ... , 8 types, 32 molecules FNfnHPhpGOgoEMemBJbjDLdlAIaiCKck
#1: 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) Strain: ATCC 204508 / S288c / Gene: CCT6, TCP20, TCP6, YD9395.21, YDR188W / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39079 #2: 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) Strain: ATCC 204508 / S288c / Gene: CCT8, J1374, YJL008C / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P47079 #3: 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) Strain: ATCC 204508 / S288c / Gene: CCT7, J0804, YJL111W / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P42943 #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) Strain: ATCC 204508 / S288c / Gene: CCT5, J1752, TCP5, YJR064W / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40413 #5: 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) Strain: ATCC 204508 / S288c / Gene: BIN3, CCT2, TCP2, YIL142W / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39076 #6: Protein | Mass: 57740.449 Da / Num. of mol.: 4 / Mutation: G345D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: ANC2, CCT4, TCP4, YDL143W / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39078 #7: 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) Strain: ATCC 204508 / S288c / Gene: CCT1, TCP1, YD8142.13, YD8142B.04, YDR212W / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P12612 #8: 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) Strain: ATCC 204508 / S288c / Gene: BIN2, CCT3, J1336, TCP3, YJL014W / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P39077 |
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-Non-polymers , 3 types, 96 molecules
#9: Chemical | ChemComp-MG / #10: Chemical | ChemComp-ADP / #11: Chemical | ChemComp-BEF / |
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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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % Description: AUTHOR USED THE SF DATA FROM ENTRIES 3P9D AND 3P9E. |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MANUALLY PLACED / Resolution: 3.8→30 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2734 / WRfactor Rwork: 0.231 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7512 / SU B: 144.734 / SU ML: 0.879 / SU R Cruickshank DPI: 0.891 / SU Rfree: 0.9424 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.942 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY.
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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 max: 348.55 Å2 / Biso mean: 141.5706 Å2 / Biso min: 70.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 30020 / Refine-ID: X-RAY DIFFRACTION
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