7X0S

Human TRiC-tubulin-S3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

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.Bao, L.Wang, Y.Cong, Y.

(2023) Commun Biol 6: 531-531

  • DOI: https://doi.org/10.1038/s42003-023-04915-x
  • Primary Citation of Related Structures:  
    7WZ3, 7X0A, 7X0S, 7X0V, 7X3J, 7X3U, 7X6Q, 7X7Y

  • PubMed Abstract: 

    The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate substrate of TRiC. Here, we present an ensemble of cryo-EM structures of endogenous human TRiC throughout its ATPase cycle, with three of them revealing endogenously engaged tubulin in different folding stages. The open-state TRiC-tubulin-S1 and -S2 maps show extra density corresponding to tubulin in the cis-ring chamber of TRiC. Our structural and XL-MS analyses suggest a gradual upward translocation and stabilization of tubulin within the TRiC chamber accompanying TRiC ring closure. In the closed TRiC-tubulin-S3 map, we capture a near-natively folded tubulin-with the tubulin engaging through its N and C domains mainly with the A and I domains of the CCT3/6/8 subunits through electrostatic and hydrophilic interactions. Moreover, we also show the potential role of TRiC C-terminal tails in substrate stabilization and folding. Our study delineates the pathway and molecular mechanism of TRiC-mediated folding of tubulin along the ATPase cycle of TRiC, and may also inform the design of therapeutic agents targeting TRiC-tubulin interactions.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit zetaA [auth K],
J [auth z]
531Homo sapiensMutation(s): 0 
Gene Names: CCT6ACCT6
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PHAROS:  P40227
GTEx:  ENSG00000146731 
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UniProt GroupP40227
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit thetaB [auth J],
K [auth P]
548Homo sapiensMutation(s): 0 
Gene Names: CCT8
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GTEx:  ENSG00000156261 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit etaC [auth H],
L [auth O]
543Homo sapiensMutation(s): 1 
Gene Names: CCT7CCTH
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GTEx:  ENSG00000135624 
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UniProt GroupQ99832
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit gammaD [auth G],
M [auth N]
545Homo sapiensMutation(s): 0 
Gene Names: CCT3CCTG
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GTEx:  ENSG00000163468 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit epsilonE,
N [auth e]
539Homo sapiensMutation(s): 0 
Gene Names: CCT5CCTE
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GTEx:  ENSG00000150753 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit deltaF [auth I],
P [auth M]
539Homo sapiensMutation(s): 0 
Gene Names: CCT4CCTD
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GTEx:  ENSG00000115484 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit betaG [auth B],
Q [auth L]
535Homo sapiensMutation(s): 0 
Gene Names: CCT2CCTB
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GTEx:  ENSG00000166226 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit alphaH [auth A],
O [auth a]
556Homo sapiensMutation(s): 0 
Gene Names: TCP1CCT1CCTA
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chainI [auth R]444Homo sapiensMutation(s): 0 
Gene Names: TUBBTUBB5
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GTEx:  ENSG00000196230 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

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AA [auth G]
BB [auth e]
DA [auth E]
EB [auth a]
GA [auth I]
AA [auth G],
BB [auth e],
DA [auth E],
EB [auth a],
GA [auth I],
HB [auth M],
JA [auth B],
KB [auth L],
MA [auth A],
PA [auth z],
R [auth K],
SA [auth P],
U [auth J],
X [auth H],
XA [auth O],
YA [auth N]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AF3 (Subject of Investigation/LOI)
Query on AF3

Download Ideal Coordinates CCD File 
AB [auth N]
CA [auth G]
DB [auth e]
FA [auth E]
GB [auth a]
AB [auth N],
CA [auth G],
DB [auth e],
FA [auth E],
GB [auth a],
IA [auth I],
JB [auth M],
LA [auth B],
MB [auth L],
OA [auth A],
RA [auth z],
T [auth K],
UA [auth P],
W [auth J],
WA [auth O],
Z [auth H]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth G]
CB [auth e]
EA [auth E]
FB [auth a]
HA [auth I]
BA [auth G],
CB [auth e],
EA [auth E],
FB [auth a],
HA [auth I],
IB [auth M],
KA [auth B],
LB [auth L],
NA [auth A],
QA [auth z],
S [auth K],
TA [auth P],
V [auth J],
VA [auth O],
Y [auth H],
ZA [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB29040300

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references
  • Version 1.2: 2024-06-26
    Changes: Data collection