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

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Jin M, Han W, Liu C, Zang Y, Li J, Wang F, Wang Y, Cong Y
OpenAccess logo Proc Natl Acad Sci U S A 116 19513-19522 (2019)
Related entries: 6krd, 6kre, 6ks6, 6ks8

Cited: 21 times
EuropePMC logo PMID: 31492816

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.

Articles - 6ks7 mentioned but not cited (1)

  1. State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I. Prog Biophys Mol Biol 160 104-120 (2021)


Reviews citing this publication (5)

  1. The structural basis of T-cell receptor (TCR) activation: An enduring enigma. Mariuzza RA, Agnihotri P, Orban J. J Biol Chem 295 914-925 (2020)
  2. Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior. Zhang Y, Doruker P, Kaynak B, Zhang S, Krieger J, Li H, Bahar I. Curr Opin Struct Biol 62 14-21 (2020)
  3. The TRiCky Business of Protein Folding in Health and Disease. Ghozlan H, Cox A, Nierenberg D, King S, Khaled AR. Front Cell Dev Biol 10 906530 (2022)
  4. How do Chaperones Bind (Partly) Unfolded Client Proteins? Sučec I, Bersch B, Schanda P. Front Mol Biosci 8 762005 (2021)
  5. Mechanistic insights into protein folding by the eukaryotic chaperonin complex CCT. Smith TM, Willardson BM. Biochem Soc Trans 50 1403-1414 (2022)

Articles citing this publication (15)

  1. Upregulated YB-1 protein promotes glioblastoma growth through a YB-1/CCT4/mLST8/mTOR pathway. Wang JZ, Zhu H, You P, Liu H, Wang WK, Fan X, Yang Y, Xu K, Zhu Y, Li Q, Wu P, Peng C, Wong CC, Li K, Shi Y, Zhang N, Wang X, Zeng R, Huang Y, Yang L, Wang Z, Hui J. J Clin Invest 132 e146536 (2022)
  2. Snapshots of actin and tubulin folding inside the TRiC chaperonin. Kelly JJ, Tranter D, Pardon E, Chi G, Kramer H, Happonen L, Knee KM, Janz JM, Steyaert J, Bulawa C, Paavilainen VO, Huiskonen JT, Yue WW. Nat Struct Mol Biol 29 420-429 (2022)
  3. Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules. Nierzwicki Ł, Palermo G. Front Mol Biosci 8 641208 (2021)
  4. Distinct architecture and composition of mouse axonemal radial spoke head revealed by cryo-EM. Zheng W, Li F, Ding Z, Liu H, Zhu L, Xu C, Li J, Gao Q, Wang Y, Fu Z, Peng C, Yan X, Zhu X, Cong Y. Proc Natl Acad Sci U S A 118 e2021180118 (2021)
  5. Human Papillomavirus infection requires the CCT Chaperonin Complex. Bugnon Valdano M, Massimi P, Broniarczyk J, Pim D, Myers M, Gardiol D, Banks L. J Virol 95 JVI.01943-20 (2021)
  6. Anticarin-β shows a promising anti-osteosarcoma effect by specifically inhibiting CCT4 to impair proteostasis. Wang G, Zhang M, Meng P, Long C, Luo X, Yang X, Wang Y, Zhang Z, Mwangi J, Kamau PM, Dai Z, Ke Z, Zhang Y, Chen W, Zhao X, Ge F, Lv Q, Rong M, Li D, Jin Y, Sheng X, Lai R. Acta Pharm Sin B 12 2268-2279 (2022)
  7. CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin. Zhao Y, Schmid MF, Frydman J, Chiu W. Nat Commun 12 4754 (2021)
  8. Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling. Dokainish HM, Sugita Y. Int J Mol Sci 22 E270 (2020)
  9. Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns. Collier MP, Moreira KB, Li KH, Chen YC, Itzhak D, Samant R, Leitner A, Burlingame A, Frydman J. Sci Rep 11 13084 (2021)
  10. Pathway and mechanism of tubulin folding mediated by TRiC/CCT along its ATPase cycle revealed using cryo-EM. Liu C, Jin M, Wang S, Han W, Zhao Q, Wang Y, Xu C, Diao L, Yin Y, Peng C, Peng C, Bao L, Wang Y, Cong Y. Commun Biol 6 531 (2023)
  11. Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT. Han W, Jin M, Liu C, Zhao Q, Wang S, Wang Y, Yin Y, Peng C, Wang Y, Cong Y. Sci Adv 9 eade1207 (2023)
  12. CryoEM structural exploration of catalytically active enzyme pyruvate carboxylase. López-Alonso JP, Lázaro M, Gil-Cartón D, Choi PH, Dodu A, Tong L, Valle M. Nat Commun 13 6185 (2022)
  13. A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle. Park J, Kim H, Gestaut D, Lim S, Opoku-Nsiah KA, Leitner A, Frydman J, Roh SH. Nat Commun 15 1007 (2024)
  14. Single-molecule visualization determines conformational substate ensembles in β-sheet-rich peptide fibrils. Zhang W, Wang R, Liu M, Li S, Vokoun AE, Deng W, Dupont RL, Zhang F, Li S, Wang Y, Liu Z, Zheng Y, Liu S, Yang Y, Wang C, Yu L, Yao Y, Wang X, Wang C. Sci Adv 9 eadg7943 (2023)
  15. Structural basis of substrate progression through the bacterial chaperonin cycle. Gardner S, Darrow MC, Lukoyanova N, Thalassinos K, Saibil HR. Proc Natl Acad Sci U S A 120 e2308933120 (2023)


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