Folding of S6 structures with divergent amino-acid composition: pathway flexibility within partly overlapping foldons

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Folding of S6 Structures with Divergent Amino Acid Composition: Pathway Flexibility within Partly Overlapping Foldons.

Olofsson, M.Hansson, S.Hedberg, L.Logan, D.T.Oliveberg, M.

(2007) J Mol Biol 365: 237

  • DOI: https://doi.org/10.1016/j.jmb.2006.09.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Studies of circular permutants have demonstrated that the folding reaction of S6 from Thermus thermophilus (S6(T)) is malleable and responds in an ordered manner to changes of the sequence separation between interacting residues: the S6(T) permutants retain a common nucleation pattern in the form of a two-strand-helix motif that can be recruited from different parts of the structure. To further test the robustness of the two-strand-helix nucleus we have here determined the crystal structure and folding reaction of an evolutionary divergent S6 protein from the hyperthermophilic bacterium Aquifex aeolicus (S6(A)). Although the overall topology of S6(A) is very similar to that of S6(T) the architecture of the hydrophobic core is radically different by containing a large proportion of stacked Phe side-chains. Despite this disparate core composition, the folding rate constant and the kinetic m values of S6(A) are identical to those of S6(T). The folding nucleus of S6(A) is also found to retain the characteristic two-strand-helix motif of the S6(T) permutants, but with a new structural emphasis. The results suggest that the protein folding reaction is linked to topology only in the sense that the native-state topology determines the repertoire of accessible nucleation motifs. If the native structure allows several equivalent ways of recruiting a productive nucleus the folding reaction is free to redistribute within these topological constraints.

  • Organizational Affiliation

    Department of Biochemistry, Umeå University, SE-901 87 Umeå, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6110Aquifex aeolicusMutation(s): 0 
Find proteins for O66474 (Aquifex aeolicus (strain VF5))
Explore O66474 
Go to UniProtKB:  O66474
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66474
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.57α = 90
b = 75.57β = 90
c = 55.5γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description