7TUB

The beta-tubulin folding intermediate IV

  • Classification: CHAPERONE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2022-02-02 Released: 2022-12-28 
  • Deposition Author(s): Zhao, Y., Frydman, J., Chiu, W.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT.

Gestaut, D.Zhao, Y.Park, J.Ma, B.Leitner, A.Collier, M.Pintilie, G.Roh, S.H.Chiu, W.Frydman, J.

(2022) Cell 185: 4770-4787.e20

  • DOI: https://doi.org/10.1016/j.cell.2022.11.014
  • Primary Citation of Related Structures:  
    7TRG, 7TTN, 7TTT, 7TUB, 7WU7

  • PubMed Abstract: 

    The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. Cryo-EM resolves four near-atomic-resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Intrinsically disordered CCT C termini within the chamber promote subsequent folding of tubulin's core and middle domains and GTP-binding. Thus, TRiC's chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates.


  • Organizational Affiliation

    Department of Biology, Stanford University, Stanford, CA 94305, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain444Homo sapiensMutation(s): 0 
Gene Names: TUBBTUBB5OK/SW-cl.56
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Find proteins for P07437 (Homo sapiens)
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PHAROS:  P07437
GTEx:  ENSG00000196230 
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UniProt GroupP07437
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit theta547Homo sapiensMutation(s): 0 
Gene Names: CCT8C21orf112CCTQKIAA0002
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Find proteins for P50990 (Homo sapiens)
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PHAROS:  P50990
GTEx:  ENSG00000156261 
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UniProt GroupP50990
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit eta553Homo sapiensMutation(s): 0 
Gene Names: CCT7CCTHNIP7-1
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PHAROS:  Q99832
GTEx:  ENSG00000135624 
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UniProt GroupQ99832
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit epsilon541Homo sapiensMutation(s): 0 
Gene Names: CCT5CCTEKIAA0098
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Find proteins for P48643 (Homo sapiens)
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PHAROS:  P48643
GTEx:  ENSG00000150753 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit beta535Homo sapiensMutation(s): 0 
Gene Names: CCT299D8.1CCTB
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PHAROS:  P78371
GTEx:  ENSG00000166226 
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UniProt GroupP78371
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit delta539Homo sapiensMutation(s): 0 
Gene Names: CCT4CCTDSRB
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Find proteins for P50991 (Homo sapiens)
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GTEx:  ENSG00000115484 
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UniProt GroupP50991
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit alpha556Homo sapiensMutation(s): 0 
Gene Names: TCP1CCT1CCTA
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Find proteins for P17987 (Homo sapiens)
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PHAROS:  P17987
GTEx:  ENSG00000120438 
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UniProt GroupP17987
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit gamma545Homo sapiensMutation(s): 0 
Gene Names: CCT3CCTGTRIC5
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Find proteins for P49368 (Homo sapiens)
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GTEx:  ENSG00000163468 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit zeta531Homo sapiensMutation(s): 0 
Gene Names: CCT6ACCT6CCTZ
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Find proteins for P40227 (Homo sapiens)
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GTEx:  ENSG00000146731 
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UniProt GroupP40227
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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 
CA [auth H]
FA [auth I]
K [auth B]
N [auth C]
Q [auth D]
CA [auth H],
FA [auth I],
K [auth B],
N [auth C],
Q [auth D],
T [auth E],
W [auth F],
Z [auth G]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AF3 (Subject of Investigation/LOI)
Query on AF3

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
GA [auth I]
L [auth B]
O [auth C]
AA [auth G],
DA [auth H],
GA [auth I],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth H]
EA [auth I]
J [auth B]
M [auth C]
P [auth D]
BA [auth H],
EA [auth I],
J [auth B],
M [auth C],
P [auth D],
S [auth E],
V [auth F],
Y [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM074074
National Institutes of Health/Office of the DirectorUnited StatesP41GM103832
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release