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- EMDB-18933: Human open TRiC with one PFD in HHT-treated cells -

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Basic information

Entry
Database: EMDB / ID: EMD-18933
TitleHuman open TRiC with one PFD in HHT-treated cells
Map data
Sample
  • Cell: Human open TRiC with one PFD in HHT-treated cells
Keywordshuman / chaperone / TRiC/CCT / folding / homoharringtonine / apoptosis
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 12.5 Å
AuthorsXing H / Beck M
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nature / Year: 2025
Title: In situ analysis reveals the TRiC duty cycle and PDCD5 as an open-state cofactor.
Authors: Huaipeng Xing / Remus R E Rosenkranz / Piere Rodriguez-Aliaga / Ting-Ting Lee / Tomáš Majtner / Stefanie Böhm / Beata Turoňová / Judith Frydman / Martin Beck /
Abstract: The ring-shaped chaperonin T-complex protein ring complex (TRiC; also known as chaperonin containing TCP-1, CCT) is an ATP-driven protein-folding machine that is essential for maintenance of cellular ...The ring-shaped chaperonin T-complex protein ring complex (TRiC; also known as chaperonin containing TCP-1, CCT) is an ATP-driven protein-folding machine that is essential for maintenance of cellular homeostasis. Its dysfunction is related to cancer and neurodegenerative disease. Despite its importance, how TRiC works in the cell remains unclear. Here we structurally analysed the architecture, conformational dynamics and spatial organization of the chaperonin TRiC in human cells using cryo-electron tomography. We resolved distinctive open, closed, substrate-bound and prefoldin-associated states of TRiC, and reconstructed its duty cycle in situ. The substrate-bound open and symmetrically closed TRiC states were equally abundant. Closed TRiC containing substrate forms distinctive clusters, indicative of spatial organization. Translation inhibition did not fundamentally change the distribution of duty cycle intermediates, but reduced substrate binding for all states as well as cluster formation. From our in-cell structures, we identified the programmed cell death protein 5 (PDCD5) as an interactor that specifically binds to almost all open but not closed TRiC, in a position that is compatible with both substrate and prefoldin binding. Our data support a model in which TRiC functions at near full occupancy to fold newly synthesized proteins inside cells. Defining the TRiC cycle and function inside cells lays the foundation to understand its dysfunction during cancer and neurodegeneration.
History
DepositionNov 17, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18933.png

Downloads & links

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Map

FileDownload / File: emd_18933.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.38 Å/pix.
x 128 pix.
= 304.128 Å		2.38 Å/pix.
x 128 pix.
= 304.128 Å		2.38 Å/pix.
x 128 pix.
= 304.128 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.376 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.29668468 - 0.7576833
Average (Standard dev.)0.023793714 (±0.11218584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 304.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18933_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_18933_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Human open TRiC with one PFD in HHT-treated cells

EntireName: Human open TRiC with one PFD in HHT-treated cells
Components
  • Cell: Human open TRiC with one PFD in HHT-treated cells

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Supramolecule #1: Human open TRiC with one PFD in HHT-treated cells

SupramoleculeName: Human open TRiC with one PFD in HHT-treated cells / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 2.46 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1287
ExtractionNumber tomograms: 352 / Number images used: 352000
Final angle assignmentType: OTHER

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