4V81

The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.307 
  • R-Value Observed: 0.309 

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Literature

The crystal structure of yeast CCT reveals intrinsic asymmetry of eukaryotic cytosolic chaperonins.

Dekker, C.Roe, S.M.McCormack, E.A.Beuron, F.Pearl, L.H.Willison, K.R.

(2011) EMBO J 30: 3078-3090

  • DOI: https://doi.org/10.1038/emboj.2011.208
  • Primary Citation of Related Structures:  
    4V81

  • PubMed Abstract: 

    The cytosolic chaperonin CCT is a 1-MDa protein-folding machine essential for eukaryotic life. The CCT interactome shows involvement in folding and assembly of a small range of proteins linked to essential cellular processes such as cytoskeleton assembly and cell-cycle regulation. CCT has a classic chaperonin architecture, with two heterogeneous 8-membered rings stacked back-to-back, enclosing a folding cavity. However, the mechanism by which CCT assists folding is distinct from other chaperonins, with no hydrophobic wall lining a potential Anfinsen cage, and a sequential rather than concerted ATP hydrolysis mechanism. We have solved the crystal structure of yeast CCT in complex with actin at 3.8 Å resolution, revealing the subunit organisation and the location of discrete patches of co-evolving 'signature residues' that mediate specific interactions between CCT and its substrates. The intrinsic asymmetry is revealed by the structural individuality of the CCT subunits, which display unique configurations, substrate binding properties, ATP-binding heterogeneity and subunit-subunit interactions. The location of the evolutionarily conserved N-terminus of Cct5 on the outside of the barrel, confirmed by mutational studies, is unique to eukaryotic cytosolic chaperonins.


  • Organizational Affiliation

    Section of Cell and Molecular Biology, Chester Beatty Laboratories, Institute of Cancer Research, London, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit alphaA,
I,
Q [auth a],
Y [auth i]
559Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CCT1TCP1YD8142.13YD8142B.04YDR212W
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit betaB,
J,
R [auth b],
Z [auth j]
527Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: BIN3CCT2TCP2YIL142W
UniProt
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UniProt GroupP39076
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit gammaAA [auth k],
C,
K,
S [auth c]
590Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: BIN2CCT3J1336TCP3YJL014W
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit deltaBA [auth l],
D,
L,
T [auth d]
528Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ANC2CCT4TCP4YDL143W
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit epsilonCA [auth m],
E,
M,
U [auth e]
562Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CCT5J1752TCP5YJR064W
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit zetaDA [auth n],
F,
N,
V [auth f]
546Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CCT6TCP20TCP6YD9395.21YDR188W
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit etaEA [auth o],
G,
O,
W [auth g]
550Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CCT7J0804YJL111W
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit thetaFA [auth p],
H,
P,
X [auth h]
568Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CCT8J1374YJL008C
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AB [auth L]
BC [auth l]
CB [auth M]
DC [auth m]
EB [auth N]
AB [auth L],
BC [auth l],
CB [auth M],
DC [auth m],
EB [auth N],
FC [auth n],
GA [auth A],
HB [auth P],
IA [auth B],
IC [auth p],
JB [auth a],
KA [auth C],
LB [auth b],
MA [auth D],
OA [auth E],
PB [auth e],
QA [auth F],
RB [auth f],
SA [auth G],
TB [auth g],
UA [auth H],
VB [auth h],
XA [auth J],
ZB [auth k]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
GB [auth O]
HC [auth o]
NB [auth c]
OB [auth d]
WA [auth I]
GB [auth O],
HC [auth o],
NB [auth c],
OB [auth d],
WA [auth I],
XB [auth i],
YB [auth j],
ZA [auth K]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BEF
Query on BEF

Download Ideal Coordinates CCD File 
AC [auth k]
BB [auth L]
CC [auth l]
DB [auth M]
EC [auth m]
AC [auth k],
BB [auth L],
CC [auth l],
DB [auth M],
EC [auth m],
FB [auth N],
GC [auth n],
HA [auth A],
IB [auth P],
JA [auth B],
JC [auth p],
KB [auth a],
LA [auth C],
MB [auth b],
NA [auth D],
PA [auth E],
QB [auth e],
RA [auth F],
SB [auth f],
TA [auth G],
UB [auth g],
VA [auth H],
WB [auth h],
YA [auth J]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.307 
  • R-Value Observed: 0.309 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.1α = 85.23
b = 162.54β = 81.15
c = 268.1γ = 61.17
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description