2J5A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2006.09.016

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
A
110Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: rpsF
Find proteins for O66474 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66474
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.570α = 90.00
b = 75.570β = 90.00
c = 55.500γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance