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- EMDB-0758: TRiC at 0.2 mM ADP-AlFx, Conformation 1, 0.2-C1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0758
TitleTRiC at 0.2 mM ADP-AlFx, Conformation 1, 0.2-C1
Map data
SampleTRiC complex
  • (T-complex protein 1 subunit ...) x 7
  • fusion protein of T-complex protein 1 subunit gamma,rep-His-CBP and T-complex protein 1 subunit gamma
  • (ligand) x 4
Function / homology
Function and homology information


Neutrophil degranulation / Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperonin-containing T-complex / unfolded protein binding / protein folding / ATP binding / plasma membrane / cytoplasm
TCP-1-like chaperonin intermediate domain superfamily / T-complex protein 1, eta subunit / Chaperonins TCP-1 signature 2. / Chaperonins TCP-1 signature 1. / TCP-1/cpn60 chaperonin family / GroEL-like equatorial domain superfamily / GroEL-like apical domain superfamily / Chaperone tailless complex polypeptide 1 (TCP-1) / T-complex protein 1, zeta subunit / T-complex protein 1, theta subunit ...TCP-1-like chaperonin intermediate domain superfamily / T-complex protein 1, eta subunit / Chaperonins TCP-1 signature 2. / Chaperonins TCP-1 signature 1. / TCP-1/cpn60 chaperonin family / GroEL-like equatorial domain superfamily / GroEL-like apical domain superfamily / Chaperone tailless complex polypeptide 1 (TCP-1) / T-complex protein 1, zeta subunit / T-complex protein 1, theta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, delta subunit / T-complex protein 1, beta subunit / T-complex protein 1, alpha subunit / Chaperonin Cpn60/TCP-1 family / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3.
T-complex protein 1 subunit alpha / T-complex protein 1 subunit beta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit delta / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit eta / T-complex protein 1 subunit theta
Biological speciesSaccharomyces cerevisiae S288C (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsJin M / 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.
Validation ReportPDB-ID: 6ks6

SummaryFull reportAbout validation report
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: 0.005
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ks6
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0758.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 512 pix.
= 337.408 Å
0.66 Å/pix.
x 512 pix.
= 337.408 Å
0.66 Å/pix.
x 512 pix.
= 337.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.659 Å
Density
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.02401147 - 0.04818636
Average (Standard dev.)0.00008942386 (±0.0014266719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 337.408 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6590.6590.659
M x/y/z512512512
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/NS512512512
D min/max/mean-0.0240.0480.000

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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 0.2 mM ADP-AlFx / Number of components: 13

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Component #1: protein, TRiC complex

ProteinName: TRiC complex / Details: TRiC complex at 0.2 mM ADP-AlFx / Recombinant expression: No
MassTheoretical: 960 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

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Component #2: protein, T-complex protein 1 subunit alpha

ProteinName: T-complex protein 1 subunit alpha / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 60.557566 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #3: protein, T-complex protein 1 subunit beta

ProteinName: T-complex protein 1 subunit beta / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 57.276254 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #4: protein, T-complex protein 1 subunit delta

ProteinName: T-complex protein 1 subunit delta / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 57.68241 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #5: protein, T-complex protein 1 subunit epsilon

ProteinName: T-complex protein 1 subunit epsilon / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 61.995004 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #6: protein, fusion protein of T-complex protein 1 subunit gamma,rep-...

ProteinName: fusion protein of T-complex protein 1 subunit gamma,rep-His-CBP and T-complex protein 1 subunit gamma
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 65.423387 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #7: protein, T-complex protein 1 subunit eta

ProteinName: T-complex protein 1 subunit eta / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 59.802438 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #8: protein, T-complex protein 1 subunit theta

ProteinName: T-complex protein 1 subunit theta / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 61.735102 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #9: protein, T-complex protein 1 subunit zeta

ProteinName: T-complex protein 1 subunit zeta / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 59.997559 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: S288c

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Component #10: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #11: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #12: ligand, ALUMINUM FLUORIDE

LigandName: ALUMINUM FLUORIDEAluminium fluoride / Number of Copies: 14 / Recombinant expression: No
MassTheoretical: 8.397705 MDa

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Component #13: ligand, water

LigandName: water / Number of Copies: 14 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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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: 277360
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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