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: 3.80 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3P9D 3P9E


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: https://doi.org/10.1016/j.str.2012.03.007
  • Primary Citation of Related Structures:  
    4V94

  • 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. 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit zetaA [auth F],
I [auth N],
Q [auth f],
Y [auth n]
546Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CCT6TCP20TCP6YD9395.21YDR188W
UniProt
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UniProt GroupP39079
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit thetaB [auth H],
J [auth P],
R [auth h],
Z [auth p]
568Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CCT8J1374YJL008C
UniProt
Find proteins for P47079 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP47079
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit etaAA [auth o],
C [auth G],
K [auth O],
S [auth g]
550Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CCT7J0804YJL111W
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit epsilonBA [auth m],
D [auth E],
L [auth M],
T [auth e]
562Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CCT5J1752TCP5YJR064W
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit betaCA [auth j],
E [auth B],
M [auth J],
U [auth b]
527Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BIN3CCT2TCP2YIL142W
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit deltaDA [auth l],
F [auth D],
N [auth L],
V [auth d]
528Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: ANC2CCT4TCP4YDL143W
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit alphaEA [auth i],
G [auth A],
O [auth I],
W [auth a]
559Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CCT1TCP1YD8142.13YD8142B.04YDR212W
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
T-complex protein 1 subunit gammaFA [auth k],
H [auth C],
P [auth K],
X [auth c]
590Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BIN2CCT3J1336TCP3YJL014W
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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AC [auth K]
BD [auth n]
CB [auth C]
DC [auth f]
ED [auth p]
AC [auth K],
BD [auth n],
CB [auth C],
DC [auth f],
ED [auth p],
FB [auth N],
GC [auth h],
HA [auth F],
HD [auth o],
IB [auth P],
JC [auth g],
KA [auth H],
KD [auth m],
LB [auth O],
MC [auth e],
NA [auth G],
ND [auth j],
OB [auth M],
PC [auth b],
QA [auth E],
QD [auth l],
RB [auth J],
SC [auth d],
TA [auth B],
TD [auth i],
UB [auth L],
VC [auth a],
WA [auth D],
WD [auth k],
XB [auth I],
YC [auth c],
ZA [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF
Query on BEF

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AB [auth A]
BC [auth K]
CD [auth n]
DB [auth C]
EC [auth f]
AB [auth A],
BC [auth K],
CD [auth n],
DB [auth C],
EC [auth f],
FD [auth p],
GB [auth N],
HC [auth h],
IA [auth F],
ID [auth o],
JB [auth P],
KC [auth g],
LA [auth H],
LD [auth m],
MB [auth O],
NC [auth e],
OA [auth G],
OD [auth j],
PB [auth M],
QC [auth b],
RA [auth E],
RD [auth l],
SB [auth J],
TC [auth d],
UA [auth B],
UD [auth i],
VB [auth L],
WC [auth a],
XA [auth D],
XD [auth k],
YB [auth I],
ZC [auth c]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG
Query on MG

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AD [auth n]
BB [auth C]
CC [auth f]
DD [auth p]
EB [auth N]
AD [auth n],
BB [auth C],
CC [auth f],
DD [auth p],
EB [auth N],
FC [auth h],
GA [auth F],
GD [auth o],
HB [auth P],
IC [auth g],
JA [auth H],
JD [auth m],
KB [auth O],
LC [auth e],
MA [auth G],
MD [auth j],
NB [auth M],
OC [auth b],
PA [auth E],
PD [auth l],
QB [auth J],
RC [auth d],
SA [auth B],
SD [auth i],
TB [auth L],
UC [auth a],
VA [auth D],
VD [auth k],
WB [auth I],
XC [auth c],
YA [auth A],
ZB [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction

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: 2024-02-28
    Changes: Data collection, Database references, Derived calculations