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- EMDB-0762: TRiC at 0.1 mM ADP-AlFx, Conformation 2b, 0.1-C2b -

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Basic information

Entry
Database: EMDB / ID: EMD-0762
TitleTRiC at 0.1 mM ADP-AlFx, Conformation 2b, 0.1-C2b
Map dataTRiC at 0.1 mM ADP-AlFx, Conformation 2b, 0.1-C2b
Sample
  • Complex: TRiC complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.67 Å
AuthorsJin ML / Cong Y
Funding support China, 4 items
OrganizationGrant numberCountry
National Basic Research Program of China(973 Program)2017YFA0503503 China
National Natural Science Foundation of China31872714 China
National Natural Science Foundation of China31670754 China
National Natural Science Foundation of China31861143028 China
CitationJournal: 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
DepositionAug 23, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateSep 18, 2019-
Current statusSep 18, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.14
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0762.png

Downloads & links

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Map

FileDownload / File: emd_0762.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTRiC at 0.1 mM ADP-AlFx, Conformation 2b, 0.1-C2b
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: 1.14 / Movie #1: 1.14
Minimum - Maximum-1.4264258 - 2.323327
Average (Standard dev.)0.02907696 (±0.21336254)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.408337.408337.408
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.4262.3230.029

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Supplemental data

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Sample components

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Entire : TRiC complex

EntireName: TRiC complex
Components
  • Complex: TRiC complex

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Supramolecule #1: TRiC complex

SupramoleculeName: TRiC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9 / Details: TRiC complex at 0.1 mM ADP-AlFx
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 960 KDa

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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

Concentration1 mg/mL
BufferpH: 7.5
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5gw4

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16962
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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