5GW4

Structure of Yeast NPP-TRiC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/nsmb.3309
  • Primary Citation of Related Structures:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit alpha
a, A
559Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TCP1 (CCT1)
Find proteins for P12612 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: TCP1
Go to UniProtKB:  P12612
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit beta
b, B
527Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CCT2 (BIN3, TCP2)
Find proteins for P39076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CCT2
Go to UniProtKB:  P39076
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit delta
d, D
528Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CCT4 (ANC2, TCP4)
Find proteins for P39078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CCT4
Go to UniProtKB:  P39078
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit epsilon
e, E
562Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CCT5 (TCP5)
Find proteins for P40413 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CCT5
Go to UniProtKB:  P40413
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit gamma
g, G
534Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CCT3 (BIN2, TCP3)
Find proteins for P39077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CCT3
Go to UniProtKB:  P39077
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit eta
h, H
550Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CCT7
Find proteins for P42943 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CCT7
Go to UniProtKB:  P42943
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit theta
q, Q
568Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CCT8
Find proteins for P47079 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CCT8
Go to UniProtKB:  P47079
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit zeta
z, Z
546Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CCT6 (TCP20, TCP6)
Find proteins for P39079 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39079
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Data processing, Database references