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- EMDB-9541: Structure of TRiC-AMP-PNP -

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Basic information

Entry
Database: EMDB / ID: EMD-9541
TitleStructure of TRiC-AMP-PNP
Map data
SampleYeast TRiC-AMP-PNP:
(T-complex protein 1 subunit ...) x 16
Function / homology
Function and homology information


chaperonin-containing T-complex / unfolded protein binding / protein folding / ATP binding / plasma membrane / cytoplasm
T-complex protein 1, theta subunit / GroEL-like apical domain superfamily / GroEL-like equatorial domain superfamily / Chaperonin TCP-1, conserved site / Chaperonin Cpn60/TCP-1 family / T-complex protein 1, alpha subunit / T-complex protein 1, beta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, eta subunit ...T-complex protein 1, theta subunit / GroEL-like apical domain superfamily / GroEL-like equatorial domain superfamily / Chaperonin TCP-1, conserved site / Chaperonin Cpn60/TCP-1 family / T-complex protein 1, alpha subunit / T-complex protein 1, beta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, eta subunit / TCP-1-like chaperonin intermediate domain superfamily / T-complex protein 1, zeta subunit / Chaperone tailless complex polypeptide 1 (TCP-1)
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 (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsZang Y / Jin M / Wang H / Cong Y
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2016
Title: Staggered ATP binding mechanism of eukaryotic chaperonin TRiC (CCT) revealed through high-resolution cryo-EM.
Authors: Yunxiang Zang / Mingliang Jin / Huping Wang / Zhicheng Cui / Liangliang Kong / Caixuan Liu / Yao Cong /
Abstract: The eukaryotic chaperonin TRiC (or CCT) assists in the folding of 10% of cytosolic proteins. Here we present two cryo-EM structures of Saccharomyces cerevisiae TRiC in a newly identified nucleotide ...The eukaryotic chaperonin TRiC (or CCT) assists in the folding of 10% of cytosolic proteins. Here we present two cryo-EM structures of Saccharomyces cerevisiae TRiC in a newly identified nucleotide partially preloaded (NPP) state and in the ATP-bound state, at 4.7-Å and 4.6-Å resolution, respectively. Through inner-subunit eGFP tagging, we identified the subunit locations in open-state TRiC and found that the CCT2 subunit pair forms an unexpected Z shape. ATP binding induces a dramatic conformational change on the CCT2 side, thereby suggesting that CCT2 plays an essential role in TRiC allosteric cooperativity. Our structural and biochemical data reveal a staggered ATP binding mechanism of TRiC with preloaded nucleotide on the CCT6 side of NPP-TRiC and demonstrate that TRiC has evolved into a complex that is structurally divided into two sides. This work offers insight into how the TRiC nucleotide cycle coordinates with its mechanical cycle in preparing folding intermediates for further productive folding.
Validation ReportPDB-ID: 5gw5

SummaryFull reportAbout validation report
History
DepositionSep 27, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseOct 26, 2016-
UpdateDec 13, 2017-
Current statusDec 13, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.921
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.921
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5gw5
  • Surface level: 0.921
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9541.map.gz / Format: CCP4 / Size: 64 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 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
Contour LevelBy AUTHOR: 0.921 / Movie #1: 0.921
Minimum - Maximum-1.5845709 - 3.335837
Average (Standard dev.)0.028204367 (±0.16525468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
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
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-1.5853.3360.028

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Supplemental data

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Sample components

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Entire Yeast TRiC-AMP-PNP

EntireName: Yeast TRiC-AMP-PNP / Details: Yeast TRiC ATP-binding state / Number of components: 17

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Component #1: protein, Yeast TRiC-AMP-PNP

ProteinName: Yeast TRiC-AMP-PNP / Details: Yeast TRiC ATP-binding state / Recombinant expression: No
MassTheoretical: 960 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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

ProteinName: T-complex protein 1 subunit alpha / Recombinant expression: No

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

ProteinName: T-complex protein 1 subunit beta / Recombinant expression: No

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

ProteinName: T-complex protein 1 subunit delta / Recombinant expression: No

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

ProteinName: T-complex protein 1 subunit epsilon / Recombinant expression: No

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Component #6: protein, T-complex protein 1 subunit gamma

ProteinName: T-complex protein 1 subunit gamma / Recombinant expression: No

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

ProteinName: T-complex protein 1 subunit eta / Recombinant expression: No

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

ProteinName: T-complex protein 1 subunit theta / Recombinant expression: No

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

ProteinName: T-complex protein 1 subunit zeta / Recombinant expression: No

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Component #10: 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: ATCC 204508 / S288c

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Component #11: 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: ATCC 204508 / S288c

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Component #12: 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: ATCC 204508 / S288c

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Component #13: 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: ATCC 204508 / S288c

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Component #14: protein, T-complex protein 1 subunit gamma

ProteinName: T-complex protein 1 subunit gamma / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 58.889094 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: 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: ATCC 204508 / S288c

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Component #16: 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: ATCC 204508 / S288c

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Component #17: 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: ATCC 204508 / S288c

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.7 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 100 % / Details: blot for 3 seconds before plunging.

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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
LensMagnification: 18000.0 X (nominal), 18000.0 X (calibrated) / Cs: 0.005 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 67990
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Output model

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