4V8R

The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

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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: 3P9D


Literature

The Crystal Structures of the Eukaryotic Chaperonin Cct Reveal its Functional Partitioning

Kalisman, N.Schroder, G.F.Levitt, M.

(2013) Structure 21: 540

  • DOI: https://doi.org/10.1016/j.str.2013.01.017
  • Primary Citation of Related Structures:  
    4B2T, 4V8R

  • PubMed Abstract: 

    In eukaryotes, CCT is essential for the correct and efficient folding of many cytosolic proteins, most notably actin and tubulin. Structural studies of CCT have been hindered by the failure of standard crystallographic analysis to resolve its eight different subunit types at low resolutions. Here, we exhaustively assess the R value fit of all possible CCT models to available crystallographic data of the closed and open forms with resolutions of 3.8 Å and 5.5 Å, respectively. This unbiased analysis finds the native subunit arrangements with overwhelming significance. The resulting structures provide independent crystallographic proof of the subunit arrangement of CCT and map major asymmetrical features of the particle onto specific subunits. The actin and tubulin substrates both bind around subunit CCT6, which shows other structural anomalies. CCT is thus clearly partitioned, both functionally and evolutionary, into a substrate-binding side that is opposite to the ATP-hydrolyzing side.


  • Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT ALPHAA [auth AA],
I [auth Aa],
Q [auth BA],
Y [auth Ba]
559Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT BETAB [auth AB],
J [auth Ab],
R [auth BB],
Z [auth Bb]
527Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT DELTAAA [auth Bd],
C [auth AD],
K [auth Ad],
S [auth BD]
528Saccharomyces cerevisiaeMutation(s): 1 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT EPSILONBA [auth Be],
D [auth AE],
L [auth Ae],
T [auth BE]
562Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT GAMMACA [auth Bg],
E [auth AG],
M [auth Ag],
U [auth BG]
590Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT ETADA [auth Bh],
F [auth AH],
N [auth Ah],
V [auth BH]
550Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT THETAEA [auth Bq],
G [auth AQ],
O [auth Aq],
W [auth BQ]
568Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT ZETAFA [auth Bz],
H [auth AZ],
P [auth Az],
X [auth BZ]
546Saccharomyces cerevisiaeMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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AD [auth Ba]
BB [auth AZ]
CC [auth BA]
DD [auth Bb]
EB [auth Aa]
AD [auth Ba],
BB [auth AZ],
CC [auth BA],
DD [auth Bb],
EB [auth Aa],
FC [auth BB],
GA [auth AA],
GD [auth Bd],
HB [auth Ab],
IC [auth BD],
JA [auth AB],
JD [auth Be],
KB [auth Ad],
LC [auth BE],
MA [auth AD],
MD [auth Bg],
NB [auth Ae],
OC [auth BG],
PA [auth AE],
PD [auth Bh],
QB [auth Ag],
RC [auth BH],
SA [auth AG],
SD [auth Bq],
TB [auth Ah],
UC [auth BQ],
VA [auth AH],
VD [auth Bz],
WB [auth Aq],
XC [auth BZ],
YA [auth AQ],
ZB [auth Az]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF
Query on BEF

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AC [auth Az]
BD [auth Ba]
CB [auth AZ]
DC [auth BA]
ED [auth Bb]
AC [auth Az],
BD [auth Ba],
CB [auth AZ],
DC [auth BA],
ED [auth Bb],
FB [auth Aa],
GC [auth BB],
HA [auth AA],
HD [auth Bd],
IB [auth Ab],
JC [auth BD],
KA [auth AB],
KD [auth Be],
LB [auth Ad],
MC [auth BE],
NA [auth AD],
ND [auth Bg],
OB [auth Ae],
PC [auth BG],
QA [auth AE],
QD [auth Bh],
RB [auth Ag],
SC [auth BH],
TA [auth AG],
TD [auth Bq],
UB [auth Ah],
VC [auth BQ],
WA [auth AH],
WD [auth Bz],
XB [auth Aq],
YC [auth BZ],
ZA [auth AQ]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG
Query on MG

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AB [auth AQ]
BC [auth Az]
CD [auth Ba]
DB [auth AZ]
EC [auth BA]
AB [auth AQ],
BC [auth Az],
CD [auth Ba],
DB [auth AZ],
EC [auth BA],
FD [auth Bb],
GB [auth Aa],
HC [auth BB],
IA [auth AA],
ID [auth Bd],
JB [auth Ab],
KC [auth BD],
LA [auth AB],
LD [auth Be],
MB [auth Ad],
NC [auth BE],
OA [auth AD],
OD [auth Bg],
PB [auth Ae],
QC [auth BG],
RA [auth AE],
RD [auth Bh],
SB [auth Ag],
TC [auth BH],
UA [auth AG],
UD [auth Bq],
VB [auth Ah],
WC [auth BQ],
XA [auth AH],
XD [auth Bz],
YB [auth Aq],
ZC [auth BZ]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • 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
CNSrefinement

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: 2019-11-06
    Changes: Data collection, Database references