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- PDB-9cs3: TRiC-ADP-S2 state is a conformation when TRiC incubated in 1 mM ADP -

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Basic information

Entry
Database: PDB / ID: 9cs3
TitleTRiC-ADP-S2 state is a conformation when TRiC incubated in 1 mM ADP
Components(T-complex protein 1 subunit ...) x 8
KeywordsCHAPERONE / Complex / Chaperonin / ADP
Function / homology
Function and homology information


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 / : / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding ...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 / : / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / : / Chaperonins TCP-1 signature 1. ...T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsJin, M. / Cong, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2017YFA0503503 China
National Natural Science Foundation of China (NSFC)31670754, 31872714, and 31861143028 China
CitationJournal: QRB Discov / Year: 2025
Title: The conformational landscape of TRiC ring-opening and its underlying stepwise mechanism revealed by cryo-EM.
Authors: Mingliang Jin / Yunxiang Zang / Huping Wang / Yao Cong /
Abstract: The TRiC/CCT complex assists in the folding of approximately 10% of cytosolic proteins through an ATP-driven conformational cycle, playing a crucial role in maintaining protein homeostasis. Despite ...The TRiC/CCT complex assists in the folding of approximately 10% of cytosolic proteins through an ATP-driven conformational cycle, playing a crucial role in maintaining protein homeostasis. Despite our understanding of ATP-driven TRiC ring closing and substrate folding, the process and mechanisms underlying TRiC ring-opening and substrate release remain largely unexplored. In this study, by determining an ensemble of cryo-EM structures of yeast TRiC in the presence of ADP, including three intermediate transition states, we present a comprehensive picture of the TRiC ring-opening process. During this process, CCT3 detects the loss of γ-phosphate and initiates with the dynamics of its apical protrusion, and expands to the outward leaning of the consecutive CCT6/8/7/5 subunits. This is followed by significant movements of CCT2, CCT4, and especially CCT1 subunits, resulting in the opening of the TRiC rings. We also observed an unforeseen temporary separation between the two rings in the CCT2 side, coordinating the release of the originally locked CCT4 N-terminus, which potentially participates in the ring-opening process. Collectively, our study reveals a stepwise TRiC ring-opening mechanism, provides a comprehensive view of the TRiC conformational landscape, and sheds lights on its subunit specificity in sensing nucleotide status and substrate release. Our findings deepen our understanding of protein folding assisted by TRiC and may inspire new strategies for the diagnosis and treatment of related diseases.
History
DepositionJul 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)968,93916
Polymers968,93916
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#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 (brewer's 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 (brewer's yeast) / Strain: S288C / References: UniProt: P39076
#3: 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 (brewer's yeast) / Strain: S288C / References: UniProt: P40413
#4: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma


Mass: 65423.387 Da / Num. of mol.: 2
Mutation: An internal strep tag and His-tag are between residues 374 and 435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: CCT3, BIN2, TCP3, YJL014W, J1336 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39077
#5: 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 (brewer's yeast) / Strain: S288C / References: UniProt: P42943
#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 (brewer's 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 (brewer's yeast) / Strain: S288C / References: UniProt: P39079
#8: 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 (brewer's yeast) / Strain: S288C / References: UniProt: P39078

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Details

Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1TRiC at ADP state 2COMPLEXall0MULTIPLE SOURCES
2T-complex protein 1 subunit gammaCOMPLEX#41RECOMBINANT
3the other TRiC subunitsCOMPLEX#1-#3, #5-#81NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Saccharomyces cerevisiae (brewer's yeast)559292S288C
33Saccharomyces cerevisiae (brewer's yeast)559292S288C
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C
Buffer solutionpH: 7.4
SpecimenEmbedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45923 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00163446
ELECTRON MICROSCOPYf_angle_d0.38785582
ELECTRON MICROSCOPYf_dihedral_angle_d5.37554407
ELECTRON MICROSCOPYf_chiral_restr0.03910286
ELECTRON MICROSCOPYf_plane_restr0.00311016

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