3F21

Crystal structure of Zalpha in complex with d(CACGTG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ{alpha}ADAR1

Ha, S.C.Choi, J.Hwang, H.Y.Rich, A.Kim, Y.G.Kim, K.K.

(2009) Nucleic Acids Res. 37: 629-637

  • DOI: 10.1093/nar/gkn976
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and is specifically recognized by Z alpha domains identified in several Z-DNA-binding proteins. The binding of Z alpha to foreign or chromosomal DNA in various seq ...

    The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and is specifically recognized by Z alpha domains identified in several Z-DNA-binding proteins. The binding of Z alpha to foreign or chromosomal DNA in various sequence contexts is known to influence various biological functions, including the DNA-mediated innate immune response and transcriptional modulation of gene expression. For these reasons, understanding its binding mode and the conformational diversity of Z alpha bound Z-DNAs is of considerable importance. However, structural studies of Z alpha bound Z-DNA have been mostly limited to standard CG-repeat DNAs. Here, we have solved the crystal structures of three representative non-CG repeat DNAs, d(CACGTG)(2), d(CGTACG)(2) and d(CGGCCG)(2) complexed to hZ alpha(ADAR1) and compared those structures with that of hZ alpha(ADAR1)/d(CGCGCG)(2) and the Z alpha-free Z-DNAs. hZ alpha(ADAR1) bound to each of the three Z-DNAs showed a well conserved binding mode with very limited structural deviation irrespective of the DNA sequence, although varying numbers of residues were in contact with Z-DNA. Z-DNAs display less structural alterations in the Z alpha-bound state than in their free form, thereby suggesting that conformational diversities of Z-DNAs are restrained by the binding pocket of Z alpha. These data suggest that Z-DNAs are recognized by Z alpha through common conformational features regardless of the sequence and structural alterations.


    Organizational Affiliation

    Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Double-stranded RNA-specific adenosine deaminase
A, B, C
81Homo sapiensMutation(s): 0 
Gene Names: ADAR (ADAR1, DSRAD, G1P1, IFI4)
EC: 3.5.4.37
Find proteins for P55265 (Homo sapiens)
Go to Gene View: ADAR
Go to UniProtKB:  P55265
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3')D,E,F7N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.238 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.365α = 90.00
b = 87.365β = 90.00
c = 72.973γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance