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- PDB-4v94: Molecular architecture of the eukaryotic chaperonin TRiC/CCT deri... -
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Open data
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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 | |||||||||
![]() | (T-complex protein 1 subunit ...) x 8 | |||||||||
![]() | CHAPERONE / chaperonin / nano cage / protein folding / molecular chaperone / ATPase / cytosol | |||||||||
Function / homology | ![]() 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 ...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 | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.4 MB | Display | ![]() |
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Full document | ![]() | 7.7 MB | Display | |
Data in XML | ![]() | 555.6 KB | Display | |
Data in CIF | ![]() | 751.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CCT6, TCP20, TCP6, YD9395.21, YDR188W / Production host: ![]() ![]() #2: Protein | Mass: 61735.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CCT8, J1374, YJL008C / Production host: ![]() ![]() #3: Protein | Mass: 59802.438 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CCT7, J0804, YJL111W / Production host: ![]() ![]() #4: Protein | Mass: 61995.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CCT5, J1752, TCP5, YJR064W / Production host: ![]() ![]() #5: Protein | Mass: 57276.254 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: BIN3, CCT2, TCP2, YIL142W / Production host: ![]() ![]() #6: Protein | Mass: 57740.449 Da / Num. of mol.: 4 / Mutation: G345D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: ANC2, CCT4, TCP4, YDL143W / Production host: ![]() ![]() #7: Protein | Mass: 60557.566 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CCT1, TCP1, YD8142.13, YD8142B.04, YDR212W / Production host: ![]() ![]() #8: Protein | Mass: 64939.828 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: BIN2, CCT3, J1336, TCP3, YJL014W / Production host: ![]() ![]() |
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-Non-polymers , 3 types, 96 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/BEF.gif)
#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: ![]() |
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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 |
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Processing
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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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