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- PDB-6krd: TRiC at 0.05 mM ADP-AlFx, Conformation 4, 0.05-C4 -

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Basic information

Entry
Database: PDB / ID: 6krd
TitleTRiC at 0.05 mM ADP-AlFx, Conformation 4, 0.05-C4
Components(T-complex protein 1 subunit ...) x 8
KeywordsCHAPERONE / Chaperonin TRiC/CCT / Allosteric network / ATPase cycle / Conformational landscape / Cryo-EM
Function / homology
Function and homology information


chaperonin-containing T-complex / unfolded protein binding / protein folding / ATP binding / plasma membrane / cytoplasm
TCP-1/cpn60 chaperonin family / T-complex protein 1, delta subunit / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / Chaperone tailless complex polypeptide 1 (TCP-1) / T-complex protein 1, theta subunit / T-complex protein 1, eta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, zeta subunit ...TCP-1/cpn60 chaperonin family / T-complex protein 1, delta subunit / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / Chaperone tailless complex polypeptide 1 (TCP-1) / T-complex protein 1, theta subunit / T-complex protein 1, eta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, zeta subunit / T-complex protein 1, beta subunit / Chaperonin Cpn60/TCP-1 family / Chaperonin TCP-1, conserved site / T-complex protein 1, alpha subunit
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 / T-complex protein 1 subunit alpha
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.38 Å
AuthorsJin, M. / Cong, Y.
Funding support China, 4items
OrganizationGrant numberCountry
National Basic Research Program of China(973 Program)2017YFA0503503 China
National Natural Science Foundation of China31670754 China
National Natural Science Foundation of China31872714 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
a: T-complex protein 1 subunit alpha
A: T-complex protein 1 subunit alpha
b: T-complex protein 1 subunit beta
B: T-complex protein 1 subunit beta
d: T-complex protein 1 subunit delta
D: T-complex protein 1 subunit delta
e: T-complex protein 1 subunit epsilon
E: T-complex protein 1 subunit epsilon
g: T-complex protein 1 subunit gamma
G: T-complex protein 1 subunit gamma
q: T-complex protein 1 subunit theta
Q: T-complex protein 1 subunit theta
z: T-complex protein 1 subunit zeta
Z: T-complex protein 1 subunit zeta
h: T-complex protein 1 subunit eta
H: T-complex protein 1 subunit eta


Theoretical massNumber of molelcules
Total (without water)955,87116
Polymers955,87116
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area61050 Å2
ΔGint-167 kcal/mol
Surface area382100 Å2

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Components

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T-complex protein 1 subunit ... , 8 types, 16 molecules aAbBdDeEgGqQzZhH

#1: Protein T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha


Mass: 60557.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P12612
#2: Protein T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


Mass: 57276.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P39076
#3: Protein T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta


Mass: 57682.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P39078
#4: Protein T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


Mass: 61995.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P40413
#5: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma


Mass: 58889.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P39077
#6: Protein T-complex protein 1 subunit theta / TCP-1-theta / CCT-theta


Mass: 61735.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P47079
#7: Protein T-complex protein 1 subunit zeta / TCP-1-zeta / CCT-zeta


Mass: 59997.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P39079
#8: Protein T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta


Mass: 59802.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P42943

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TRiC complex / Type: COMPLEX / Details: TRiC complex at 0.05 mM ADP-AlFx / Entity ID: #1-#8 / Source: NATURAL
Molecular weightValue: 0.96 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54639 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00163836
ELECTRON MICROSCOPYf_angle_d0.36386115
ELECTRON MICROSCOPYf_dihedral_angle_d5.11954744
ELECTRON MICROSCOPYf_chiral_restr0.03910339
ELECTRON MICROSCOPYf_plane_restr0.00211080

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