5GW4

Structure of Yeast NPP-TRiC

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

  • Deposited: 2016-09-08 Released: 2016-10-26 
  • Deposition Author(s): Zang, Y., Jin, M., Wang, H., Cong, Y.
  • Funding Organization(s): CAS Pilot Strategic Science and Technology Projects B, National Natural Science Foundation of China, National Basic Research Program of China

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Staggered ATP binding mechanism of eukaryotic chaperonin TRiC (CCT) revealed through high-resolution cryo-EM.

Zang, Y.Jin, M.Wang, H.Cui, Z.Kong, L.Liu, C.Cong, Y.

(2016) Nat Struct Mol Biol 23: 1083-1091

  • DOI: https://doi.org/10.1038/nsmb.3309
  • Primary Citation of Related Structures:  
    5GW4, 5GW5

  • PubMed 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 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.


  • Organizational Affiliation

    National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 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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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
Find proteins for P40413 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit gammaI [auth g],
J [auth G]
534Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P39077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
Find proteins for P42943 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
Find proteins for P47079 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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 
UniProt
Find proteins for P39079 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
MODEL REFINEMENTCoot0.8.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CAS Pilot Strategic Science and Technology Projects BChinaXDB08030201
National Natural Science Foundation of ChinaChina31270771
National Natural Science Foundation of ChinaChina31222016
National Basic Research Program of ChinaChina2013CB910401

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Data processing, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references