4V94

Molecular architecture of the eukaryotic chaperonin TRiC/CCT derived by a combination of chemical crosslinking and mass-spectrometry, XL-MS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 3P9E - determined by Dekker, C., Roe, S.M., McCormack, E.A., Beuron, F., Pearl, L.H., Willison, K.R.  
  • 3P9D - determined by Dekker, C., Roe, S.M., McCormack, E.A., Beuron, F., Pearl, L.H., Willison, K.R.  

Literature

The Molecular Architecture of the Eukaryotic Chaperonin TRiC/CCT.

Leitner, A.Joachimiak, L.A.Bracher, A.Monkemeyer, L.Walzthoeni, T.Chen, B.Pechmann, S.Holmes, S.Cong, Y.Ma, B.Ludtke, S.Chiu, W.Hartl, F.U.Aebersold, R.Frydman, J.

(2012) Structure 20: 814-825

  • DOI: 10.1016/j.str.2012.03.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • TRiC/CCT is a highly conserved and essential chaperonin that uses ATP cycling to facilitate folding of approximately 10% of the eukaryotic proteome. This 1 MDa hetero-oligomeric complex consists of two stacked rings of eight paralogous subunits each. ...

    TRiC/CCT is a highly conserved and essential chaperonin that uses ATP cycling to facilitate folding of approximately 10% of the eukaryotic proteome. This 1 MDa hetero-oligomeric complex consists of two stacked rings of eight paralogous subunits each. Previously proposed TRiC models differ substantially in their subunit arrangements and ring register. Here, we integrate chemical crosslinking, mass spectrometry, and combinatorial modeling to reveal the definitive subunit arrangement of TRiC. In vivo disulfide mapping provided additional validation for the crosslinking-derived arrangement as the definitive TRiC topology. This subunit arrangement allowed the refinement of a structural model using existing X-ray diffraction data. The structure described here explains all available crosslink experiments, provides a rationale for previously unexplained structural features, and reveals a surprising asymmetry of charges within the chaperonin folding chamber.


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit zeta
F, N, f, n
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit theta
H, P, h, p
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: 3
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit eta
G, O, g, o
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: 4
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit epsilon
E, M, e, m
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 beta
B, J, b, j
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: 6
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit delta
D, L, d, l
528Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
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: 7
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit alpha
A, I, a, i
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: 8
MoleculeChainsSequence LengthOrganismDetails
T-complex protein 1 subunit gamma
C, K, c, k
590Saccharomyces 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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
a, A, B, b, c, C, d, D, E, e, f, F, G, g, H, h, i, I, j, J, k, K, L, l, m, M, n, N, O, o, P, p
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
a, A, B, b, C, c, D, d, E, e, f, F, G, g, h, H, i, I, j, J, K, k, l, L, m, M, N, n, O, o, p, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
a, A, b, B, C, c, D, d, E, e, F, f, G, g, H, h, i, I, j, J, k, K, l, L, m, M, n, N, o, O, p, P
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.257 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 159.100α = 85.23
b = 162.540β = 81.15
c = 268.100γ = 61.17
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2017-11-22
    Type: Refinement description