6KS6

TRiC at 0.2 mM ADP-AlFx, Conformation 1, 0.2-C1

  • Classification: CHAPERONE
  • Organism(s): Saccharomyces cerevisiae S288C
  • Mutation(s): No 

  • Deposited: 2019-08-23 Released: 2019-09-18 
  • Deposition Author(s): Jin, M., Cong, Y.
  • Funding Organization(s): National Basic Research Program of China (973 Program), National Natural Science Foundation of China

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An ensemble of cryo-EM structures of TRiC reveal its conformational landscape and subunit specificity.

Jin, M.Han, W.Liu, C.Zang, Y.Li, J.Wang, F.Wang, Y.Cong, Y.

(2019) Proc Natl Acad Sci U S A 116: 19513-19522

  • DOI: https://doi.org/10.1073/pnas.1903976116
  • Primary Citation of Related Structures:  
    6KRD, 6KRE, 6KS6, 6KS7, 6KS8

  • PubMed 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-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.


  • Organizational Affiliation

    National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit alphaA [auth a],
B [auth A]
559Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P12612 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP12612
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit betaC [auth b],
D [auth B]
527Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P39076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit deltaE [auth d],
F [auth D]
528Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P39078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit epsilonG [auth e],
H [auth E]
562Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
fusion protein of T-complex protein 1 subunit gamma,rep-His-CBP and T-complex protein 1 subunit gammaI [auth g],
J [auth G]
594Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit etaK [auth h],
L [auth H]
550Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit thetaM [auth q],
N [auth Q]
568Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit zetaO [auth z],
P [auth Z]
546Saccharomyces cerevisiae S288CMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
AB [auth q]
CA [auth d]
DB [auth Q]
EB [auth z]
FA [auth D]
AB [auth q],
CA [auth d],
DB [auth Q],
EB [auth z],
FA [auth D],
HB [auth Z],
IA [auth e],
LA [auth E],
OA [auth g],
Q [auth a],
RA [auth G],
T [auth A],
UA [auth h],
W [auth b],
XA [auth H],
Z [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AF3 (Subject of Investigation/LOI)
Query on AF3

Download Ideal Coordinates CCD File 
BA [auth B]
EA [auth d]
GB [auth z]
HA [auth D]
JB [auth Z]
BA [auth B],
EA [auth d],
GB [auth z],
HA [auth D],
JB [auth Z],
KA [auth e],
NA [auth E],
QA [auth g],
S [auth a],
TA [auth G],
V [auth A],
WA [auth h],
Y [auth b],
ZA [auth H]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth B]
BB [auth q]
CB [auth Q]
DA [auth d]
FB [auth z]
AA [auth B],
BB [auth q],
CB [auth Q],
DA [auth d],
FB [auth z],
GA [auth D],
IB [auth Z],
JA [auth e],
MA [auth E],
PA [auth g],
R [auth a],
SA [auth G],
U [auth A],
VA [auth h],
X [auth b],
YA [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2017YFA0503503
National Natural Science Foundation of ChinaChina31670754
National Natural Science Foundation of ChinaChina31872714
National Natural Science Foundation of ChinaChina31861143028

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 1.3: 2024-03-27
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations