4V8R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

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

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

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: 10.1016/j.str.2013.01.017
  • Primary Citation of Related Structures:  

  • 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 d ...

    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.


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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-COMPLEX PROTEIN 1 SUBUNIT ALPHA
AA, Aa, BA, Ba
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: 2
MoleculeChainsSequence LengthOrganismDetails
T-COMPLEX PROTEIN 1 SUBUNIT BETA
AB, Ab, BB, Bb
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: 3
MoleculeChainsSequence LengthOrganismDetails
T-COMPLEX PROTEIN 1 SUBUNIT DELTA
AD, Ad, BD, Bd
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: 4
MoleculeChainsSequence LengthOrganismDetails
T-COMPLEX PROTEIN 1 SUBUNIT EPSILON
AE, Ae, BE, Be
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 GAMMA
AG, Ag, BG, Bg
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
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
T-COMPLEX PROTEIN 1 SUBUNIT ETA
AH, Ah, BH, Bh
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: 7
MoleculeChainsSequence LengthOrganismDetails
T-COMPLEX PROTEIN 1 SUBUNIT THETA
AQ, Aq, BQ, Bq
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: 8
MoleculeChainsSequence LengthOrganismDetails
T-COMPLEX PROTEIN 1 SUBUNIT ZETA
AZ, Az, BZ, Bz
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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
AA, Aa, AB, Ab, AD, Ad, AE, Ae, Ag, AG, Ah, AH, AQ, Aq, AZ, Az, Ba, BA, BB, Bb, Bd, BD, Be, BE, Bg, BG, Bh, BH, BQ, Bq, Bz, BZ
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
AA, Aa, Ab, AB, Ad, AD, Ae, AE, Ag, AG, Ah, AH, AQ, Aq, Az, AZ, Ba, BA, Bb, BB, Bd, BD, Be, BE, Bg, BG, Bh, BH, Bq, BQ, BZ, Bz
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
Aa, AA, AB, Ab, Ad, AD, AE, Ae, Ag, AG, Ah, AH, Aq, AQ, AZ, Az, Ba, BA, BB, Bb, BD, Bd, Be, BE, BG, Bg, Bh, BH, BQ, Bq, Bz, BZ
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: 0.284 
  • R-Value Work: 0.248 
  • 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
CNSrefinement

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