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- EMDB-0764: TRiC at 0.05 mM ADP-AlFx, Conformation 1, 0.05-C1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0764
TitleTRiC at 0.05 mM ADP-AlFx, Conformation 1, 0.05-C1
Map data
SampleTRiC complex
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 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 ...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-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0764.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 196 pix.
= 258.328 Å
1.32 Å/pix.
x 196 pix.
= 258.328 Å
1.32 Å/pix.
x 196 pix.
= 258.328 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
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-1.3329618 - 2.417517
Average (Standard dev.)0.063416205 (±0.25307652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 258.328 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z258.328258.328258.328
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-1.3332.4180.063

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Supplemental data

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Sample components

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Entire TRiC complex

EntireName: TRiC complex / Details: TRiC complex at 0.05 mM ADP-AlFx / Number of components: 1

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Component #1: protein, TRiC complex

ProteinName: TRiC complex / Details: TRiC complex at 0.05 mM ADP-AlFx / Recombinant expression: No
MassTheoretical: 960 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 38 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 22705
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF

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