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Open data
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Basic information
Entry | Database: PDB / ID: 4a0w | ||||||
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Title | model built against symmetry-free cryo-EM map of TRiC-ADP-AlFx | ||||||
![]() | T-COMPLEX PROTEIN 1 SUBUNIT BETA | ||||||
![]() | CHAPERONE / CHAPERONIN / PROTEIN FOLDING | ||||||
Function / homology | ![]() Association of TriC/CCT with target proteins during biosynthesis / RHOBTB2 GTPase cycle / RHOBTB1 GTPase cycle / chaperonin-containing T-complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.9 Å | ||||||
![]() | Cong, Y. / Schroder, G.F. / Meyer, A.S. / Jakana, J. / Ma, B. / Dougherty, M.T. / Schmid, M.F. / Reissmann, S. / Levitt, M. / Ludtke, S.L. ...Cong, Y. / Schroder, G.F. / Meyer, A.S. / Jakana, J. / Ma, B. / Dougherty, M.T. / Schmid, M.F. / Reissmann, S. / Levitt, M. / Ludtke, S.L. / Frydman, J. / Chiu, W. | ||||||
![]() | ![]() Title: Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle. Authors: Yao Cong / Gunnar F Schröder / Anne S Meyer / Joanita Jakana / Boxue Ma / Matthew T Dougherty / Michael F Schmid / Stefanie Reissmann / Michael Levitt / Steven L Ludtke / Judith Frydman / Wah Chiu / ![]() Abstract: The eukaryotic group II chaperonin TRiC/CCT is a 16-subunit complex with eight distinct but similar subunits arranged in two stacked rings. Substrate folding inside the central chamber is triggered ...The eukaryotic group II chaperonin TRiC/CCT is a 16-subunit complex with eight distinct but similar subunits arranged in two stacked rings. Substrate folding inside the central chamber is triggered by ATP hydrolysis. We present five cryo-EM structures of TRiC in apo and nucleotide-induced states without imposing symmetry during the 3D reconstruction. These structures reveal the intra- and inter-ring subunit interaction pattern changes during the ATPase cycle. In the apo state, the subunit arrangement in each ring is highly asymmetric, whereas all nucleotide-containing states tend to be more symmetrical. We identify and structurally characterize an one-ring closed intermediate induced by ATP hydrolysis wherein the closed TRiC ring exhibits an observable chamber expansion. This likely represents the physiological substrate folding state. Our structural results suggest mechanisms for inter-ring-negative cooperativity, intra-ring-positive cooperativity, and protein-folding chamber closure of TRiC. Intriguingly, these mechanisms are different from other group I and II chaperonins despite their similar architecture. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1962MC ![]() 1960C ![]() 1961C ![]() 1963C ![]() 4a0oC ![]() 4a0vC ![]() 4a13C C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 55107.234 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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 |
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Sample preparation
Component | Name: BOVINE TRIC IN THE AMP- PNP STATE / Type: COMPLEX |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 4.1 mm |
Specimen holder | Temperature: 101 K |
Image recording | Electron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 300 |
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Processing
EM software | Name: EMAN / Version: 1.8 / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: EACH MICROGRAPH | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 13.9 Å / Num. of particles: 16495 / Nominal pixel size: 2.4 Å / Actual pixel size: 2.4 Å Details: OUR MODELS DO NOT INCLUDE SOME REGIONS OF THE APICAL DOMAIN IN SEVERAL SUBUNITS, BECAUSE THE MAP IN THOSE REGIONS WAS NOT VERY WELL RESOLVED DUE TO THE DYNAMIC NATURE OF THOSE SUBUNITS. WE ...Details: OUR MODELS DO NOT INCLUDE SOME REGIONS OF THE APICAL DOMAIN IN SEVERAL SUBUNITS, BECAUSE THE MAP IN THOSE REGIONS WAS NOT VERY WELL RESOLVED DUE TO THE DYNAMIC NATURE OF THOSE SUBUNITS. WE FITTED THE MODEL WITH THE OCCUPANCY REFINEMENT FEATURE IN DIREX. THIS BASICALLY DETERMINES WHETHER THERE IS SUFFICIENT DENSITY FOR EACH RESIDUE OR IF THERE IS REDUCED OR MISSING DENSITY. THE OCCUPANCY IS VALUE BETWEEN 0 AND 1. WE WROTE THIS VALUE INTO THE B-FACTOR COLUMN AS 100X(1-OCCUPANCY). THIS RESEMBLES A B-FACTOR BUT IS NOT EXACTLY THE SAME. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1962. (DEPOSITION ID: 10237). Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 13.9 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 13.9 Å
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