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- EMDB-45891: TRiC-ADP-S4 -

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Basic information

Entry
Database: EMDB / ID: EMD-45891
TitleTRiC-ADP-S4
Map dataTRiC-ADP-S4
Sample
  • Complex: TRiC at ADP state 3
    • Complex: gamma subunit
    • Complex: other TRiC subunits
KeywordsComplex / Chaperonin / ADP / CHAPERONE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.5 Å
AuthorsJin M / Cong Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0503503 China
National Natural Science Foundation of China (NSFC)31670754, 31872714, and 31861143028 China
CitationJournal: QRB Discov / Year: 2025
Title: The conformational landscape of TRiC ring-opening and its underlying stepwise mechanism revealed by cryo-EM.
Authors: Mingliang Jin / Yunxiang Zang / Huping Wang / Yao Cong /
Abstract: The TRiC/CCT complex assists in the folding of approximately 10% of cytosolic proteins through an ATP-driven conformational cycle, playing a crucial role in maintaining protein homeostasis. Despite ...The TRiC/CCT complex assists in the folding of approximately 10% of cytosolic proteins through an ATP-driven conformational cycle, playing a crucial role in maintaining protein homeostasis. Despite our understanding of ATP-driven TRiC ring closing and substrate folding, the process and mechanisms underlying TRiC ring-opening and substrate release remain largely unexplored. In this study, by determining an ensemble of cryo-EM structures of yeast TRiC in the presence of ADP, including three intermediate transition states, we present a comprehensive picture of the TRiC ring-opening process. During this process, CCT3 detects the loss of γ-phosphate and initiates with the dynamics of its apical protrusion, and expands to the outward leaning of the consecutive CCT6/8/7/5 subunits. This is followed by significant movements of CCT2, CCT4, and especially CCT1 subunits, resulting in the opening of the TRiC rings. We also observed an unforeseen temporary separation between the two rings in the CCT2 side, coordinating the release of the originally locked CCT4 N-terminus, which potentially participates in the ring-opening process. Collectively, our study reveals a stepwise TRiC ring-opening mechanism, provides a comprehensive view of the TRiC conformational landscape, and sheds lights on its subunit specificity in sensing nucleotide status and substrate release. Our findings deepen our understanding of protein folding assisted by TRiC and may inspire new strategies for the diagnosis and treatment of related diseases.
History
DepositionJul 23, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45891.png

Downloads & links

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Map

FileDownload / File: emd_45891.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRiC-ADP-S4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.408 Å		1.32 Å/pix.
x 256 pix.
= 337.408 Å		1.32 Å/pix.
x 256 pix.
= 337.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.318 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.00048980874 - 0.017514605
Average (Standard dev.)0.0003553298 (±0.0016832164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.408 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : TRiC at ADP state 3

EntireName: TRiC at ADP state 3
Components
  • Complex: TRiC at ADP state 3
    • Complex: gamma subunit
    • Complex: other TRiC subunits

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Supramolecule #1: TRiC at ADP state 3

SupramoleculeName: TRiC at ADP state 3 / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: gamma subunit

SupramoleculeName: gamma subunit / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C

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Supramolecule #3: other TRiC subunits

SupramoleculeName: other TRiC subunits / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3035
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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