1R7J

Crystal structure of the DNA-binding protein Sso10a from Sulfolobus solfataricus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The hyperthermophile protein Sso10a is a dimer of winged helix DNA-binding domains linked by an antiparallel coiled coil rod.

Chen, L., Chen, L.R., Zhou, X.E., Wang, Y., Kahsai, M.A., Clark, A.T., Edmondson, S.P., Liu, Z.J., Rose, J.P., Wang, B.C., Meehan, E.J., Shriver, J.W.

(2004) J.Mol.Biol. 341: 73-91

  • DOI: 10.1016/j.jmb.2004.05.044

  • PubMed Abstract: 

    • Sso10a is a member of a group of DNA-binding proteins thought to be important in chromatin structure and regulation in the hyperthermophilic archaeon Sulfolobus solfataricus. We have determined the structure of Sso10a to 1.47A resolution directly wit ...

    Sso10a is a member of a group of DNA-binding proteins thought to be important in chromatin structure and regulation in the hyperthermophilic archaeon Sulfolobus solfataricus. We have determined the structure of Sso10a to 1.47A resolution directly with unlabelled native crystals by a novel approach using sulfur single-wavelength anomalous scattering (SAS) from a chromium X-ray source. The 95 amino acid residue protein contains a winged helix DNA-binding domain with an extended C-terminal alpha-helix that leads to dimerization by forming a two-stranded, antiparallel coiled-coil rod. The winged helix domains are at opposite ends of the extended coiled coil with two putative DNA-recognition helices separated by 55A and rotated by 83 degrees. Formation of stable dimers in solution is demonstrated by both analytical ultracentrifugation and differential scanning calorimetry. With a T0 of 109 degrees C, Sso10a is one of the most stable two-stranded coiled coils known. The coiled coil contains a rare aspartate residue (D69) in the normally hydrophobic d position of the heptad repeat, with two aspartate-lysine (d-g') interhelical ion pairs in the symmetrical dimer. Mutation of D69 to alanine resulted in an increase in thermal stability, indicating that destabilization resulting from the partially buried aspartate residue cannot be offset by ion pair formation. Possible DNA-binding interactions are discussed on the basis of comparisons to other winged helix proteins. The structure of Sso10a provides insight into the structures of the conserved domain represented by COG3432, a group of more than 20 hypothetical transcriptional regulators coded in the genomic sequences of both crenarchaeota and euryarchaeota.

    Organizational Affiliation: 

    Laboratory for Structural Biology, University of Alabama in Huntsville, Huntsville, AL 35899, USA. chenlq@uah.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Conserved hypothetical protein Sso10a
A
95Saccharolobus solfataricusMutation(s): 0 
Gene Names: sso10a
Find proteins for Q5W1E8 (Saccharolobus solfataricus)
Go to UniProtKB:  Q5W1E8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.940α = 90.00
b = 72.300β = 90.00
c = 30.290γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
ARP/wARPmodel building
ISASphasing
HKL-2000data reduction
RESOLVEphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance