1Q3S

Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms.

Shomura, Y.Yoshida, T.Iizuka, R.Maruyama, T.Yohda, M.Miki, K.

(2004) J Mol Biol 335: 1265-1278

  • DOI: 10.1016/j.jmb.2003.11.028
  • Primary Citation of Related Structures:  
    1Q3R, 1Q3Q, 1Q2V, 1Q3S

  • PubMed Abstract: 
  • The crystal structures of the group II chaperonins consisting of the alpha subunit with amino acid substitutions of G65C and/or I125T from the hyperthermophilic archaeum Thermococcus strain KS-1 were determined. These mutants have been shown to be ac ...

    The crystal structures of the group II chaperonins consisting of the alpha subunit with amino acid substitutions of G65C and/or I125T from the hyperthermophilic archaeum Thermococcus strain KS-1 were determined. These mutants have been shown to be active in ATP hydrolysis but inactive in protein folding. The structures were shown to be double-ring hexadecamers in an extremely closed form, which was consistent with the crystal structure of native alpha8beta8-chaperonin from Thermoplasma acidophilum. Comparisons of the present structures with the atomic structures of the GroEL14-GroES7-(ADP)7 complex revealed that the deficiency in protein-folding activity with the G65C amino acid substitution is caused by the steric hindrance of the local conformational change in an equatorial domain. We concluded that this mutant chaperonin with G65C substitution is deprived of the smooth conformational change in the refolding-reaction cycle. We obtained a new form of crystal with a distinct space group at a lower concentration of sulfate ion in the presence of nucleotide. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion. Such subunit rotation has never been characterized in group II chaperonins. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion.


    Related Citations: 
    • Crystallization and preliminary X-ray characterization of archaeal group II chaperonin alpha-subunit from Thermococcus strain KS-1
      Shomura, Y., Yoshida, T., Maruyama, T., Yohda, M., Miki, K.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1830

    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thermosome alpha subunitABCDEFGH548Thermococcus sp. JCM 11816Mutation(s): 1 
Gene Names: THSA OR CPKAthsA
EC: 3.6.4.9
Find proteins for P61112 (Thermococcus sp. (strain JCM 11816 / KS-1))
Explore P61112 
Go to UniProtKB:  P61112
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B, C, D, E, F, G, H
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D, E, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.425α = 90
b = 236.23β = 90
c = 234.106γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance