+Open data
-Basic information
Entry | Database: PDB / ID: 6ks7 | |||||||||||||||
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Title | TRiC at 0.1 mM ADP-AlFx, Conformation 1, 0.1-C1 | |||||||||||||||
Components |
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Keywords | CHAPERONE / Chaperonin TRiC/CCT / Allosteric network / ATPase cycle / Conformational landscape / Cryo-EM | |||||||||||||||
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 / 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 | Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.62 Å | |||||||||||||||
Authors | Jin, M. / Cong, Y. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: An ensemble of cryo-EM structures of TRiC reveal its conformational landscape and subunit specificity. Authors: Mingliang Jin / Wenyu Han / Caixuan Liu / Yunxiang Zang / Jiawei Li / Fangfang Wang / Yanxing Wang / Yao Cong / Abstract: TRiC/CCT assists the folding of ∼10% of cytosolic proteins through an ATP-driven conformational cycle and is essential in maintaining protein homeostasis. Here, we determined an ensemble of cryo- ...TRiC/CCT assists the folding of ∼10% of cytosolic proteins through an ATP-driven conformational cycle and is essential in maintaining protein homeostasis. Here, we determined an ensemble of cryo-electron microscopy (cryo-EM) structures of yeast TRiC at various nucleotide concentrations, with 4 open-state maps resolved at near-atomic resolutions, and a closed-state map at atomic resolution, revealing an extra layer of an unforeseen N-terminal allosteric network. We found that, during TRiC ring closure, the CCT7 subunit moves first, responding to nucleotide binding; CCT4 is the last to bind ATP, serving as an ATP sensor; and CCT8 remains ADP-bound and is hardly involved in the ATPase-cycle in our experimental conditions; overall, yeast TRiC consumes nucleotide in a 2-ring positively coordinated manner. Our results depict a thorough picture of the TRiC conformational landscape and its allosteric transitions from the open to closed states in more structural detail and offer insights into TRiC subunit specificity in ATP consumption and ring closure, and potentially in substrate processing. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ks7.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ks7.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6ks7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ks7_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ks7_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6ks7_validation.xml.gz | 173 KB | Display | |
Data in CIF | 6ks7_validation.cif.gz | 273.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/6ks7 ftp://data.pdbj.org/pub/pdb/validation_reports/ks/6ks7 | HTTPS FTP |
-Related structure data
Related structure data | 0759MC 0756C 0757C 0758C 0760C 0761C 0762C 0763C 0764C 0765C 0766C 0767C 6krdC 6kreC 6ks6C 6ks8C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-T-complex protein 1 subunit ... , 8 types, 14 molecules HhaAbBdDeEqQzZ
#1: Protein | Mass: 59802.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P42943 #2: Protein | Mass: 60557.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P12612 #3: Protein | Mass: 57276.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P39076 #4: Protein | Mass: 57682.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P39078 #5: Protein | | Mass: 61995.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P40413 #6: Protein | | Mass: 56939.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P40413 #8: Protein | Mass: 61735.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P47079 #9: Protein | Mass: 59997.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P39079 |
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-Protein , 1 types, 2 molecules gG
#7: Protein | Mass: 65423.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P39077 |
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-Details
Sequence details | Authors state that rep-His-CBP tag is added between PRO g/G 374 and LYS gG 435 for CCT3 subunit. |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TRiC complex / Type: COMPLEX / Details: TRiC complex at 0.1 mM ADP-AlFx / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.96 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.10_2155: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61702 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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