1WVL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1002/prot.20524

  • 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 par ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-binding proteins 7a/7b/7d, GCN4
A, B
80Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)Mutation(s): 0 
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Go to UniProtKB:  P13123
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'C,D10N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.230 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.650α = 90.00
b = 58.650β = 90.00
c = 186.680γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
CrystalCleardata collection
CNSphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2004-12-16 
  • Released Date: 2005-08-02 
  • Deposition Author(s): Wu, S.W., Wang, A.H.

Revision History 

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance