+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0758 | |||||||||||||||
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Title | TRiC at 0.2 mM ADP-AlFx, Conformation 1, 0.2-C1 | |||||||||||||||
Map data | TRiC at 0.2 mM ADP-AlFx, Conformation 1, 0.2-C1 | |||||||||||||||
Sample |
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Keywords | Chaperonin TRiC/CCT / Allosteric network / ATPase cycle / Conformational landscape / Cryo-EM / 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 / 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 | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||||||||
Authors | Jin M / Cong Y | |||||||||||||||
Funding support | China, 4 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0758.map.gz | 23.2 MB | EMDB map data format | |
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Header (meta data) | emd-0758-v30.xml emd-0758.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
Images | emd_0758.png | 195.9 KB | ||
Filedesc metadata | emd-0758.cif.gz | 8.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0758 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0758 | HTTPS FTP |
-Validation report
Summary document | emd_0758_validation.pdf.gz | 424.7 KB | Display | EMDB validaton report |
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Full document | emd_0758_full_validation.pdf.gz | 424.3 KB | Display | |
Data in XML | emd_0758_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | emd_0758_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0758 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0758 | HTTPS FTP |
-Related structure data
Related structure data | 6ks6MC 0756C 0757C 0759C 0760C 0761C 0762C 0763C 0764C 0765C 0766C 0767C 6krdC 6kreC 6ks7C 6ks8C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0758.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TRiC at 0.2 mM ADP-AlFx, Conformation 1, 0.2-C1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.659 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : TRiC complex
+Supramolecule #1: TRiC complex
+Macromolecule #1: T-complex protein 1 subunit alpha
+Macromolecule #2: T-complex protein 1 subunit beta
+Macromolecule #3: T-complex protein 1 subunit delta
+Macromolecule #4: T-complex protein 1 subunit epsilon
+Macromolecule #5: fusion protein of T-complex protein 1 subunit gamma,rep-His-CBP a...
+Macromolecule #6: T-complex protein 1 subunit eta
+Macromolecule #7: T-complex protein 1 subunit theta
+Macromolecule #8: T-complex protein 1 subunit zeta
+Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ALUMINUM FLUORIDE
+Macromolecule #12: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 277360 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |