Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA decamer

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.276 

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Design and characterization of a multimeric DNA binding protein using Sac7d and GCN4 as templates

Wu, S.W.Ko, T.P.Chou, C.C.Wang, A.H.

(2005) Proteins 60: 617-628

  • DOI: https://doi.org/10.1002/prot.20524
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The protein Sac7d belongs to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Sac7d is extremely stable to heat, acid, and chemical agents. This protein is a monomer and it binds DNA without any particular sequence preference, while inducing a sharp kink in the DNA. By appending a leucine-zipper-like helical peptide derived from the yeast transcriptional activator GCN4 to the C-terminal end of Sac7d, the modified monomers (denoted S7dLZ) are expected to interact with each other via hydrophobic force to form a parallel dimer. The recombinant S7dLZ was expressed in Escherichia coli and purified by heating and ion-exchange chromatography. The formation of dimer was detected by gel-filtration chromatography and chemical cross-link. The results of surface plasmon resonance and circular dichroism experiments showed that the DNA-binding capacity was retained. Furthermore, X-ray diffraction analysis of single crystals of S7dLZ in complex with DNA decamer CCTATATAGG showed that the leucine-zipper segments of S7dLZ were associated into an antiparallel four-helix bundle. There are two DNA fragments bound to each S7dLZ tetramer in the crystal. This model works as a successful template that endows protein a new function without losing original properties.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-binding proteins 7a/7b/7d, GCN4C [auth A],
D [auth B]
80Sulfolobus acidocaldariusMutation(s): 0 
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore P13123 
Go to UniProtKB:  P13123
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13123
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'A [auth C],
B [auth D]
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.276 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.65α = 90
b = 58.65β = 90
c = 186.68γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
XDSdata reduction
CrystalCleardata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description