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 

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

  • 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
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT GAMMAAGAgBGBg590Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT ETAAHAhBHBh550Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT THETAAQAqBQBq568Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT ALPHAAAAaBABa559Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P12612 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT BETAABAbBBBb527Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT DELTAADAdBDBd528Saccharomyces cerevisiaeMutation(s): 1 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT EPSILONAEAeBEBe562Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
T-COMPLEX PROTEIN 1 SUBUNIT ZETAAZAzBZBz546Saccharomyces cerevisiaeMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

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AA, AB, AD, AE, AG, AH, AQ, AZ, Aa, Ab, Ad, Ae, Ag, Ah, Aq, Az, BA, BB, BD, BE, BG, BH, BQ, BZ, Ba, Bb, Bd, Be, Bg, Bh, Bq, Bz
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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

Deposition Data

Revision History 

  • 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