1QBJ

CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA.

Schwartz, T., Rould, M.A., Lowenhaupt, K., Herbert, A., Rich, A.

(1999) Science 284: 1841-1845

  • DOI: 10.1126/science.284.5421.1841
  • Primary Citation of Related Structures:  
    1QBJ

  • PubMed Abstract: 

    • The editing enzyme double-stranded RNA adenosine deaminase includes a DNA binding domain, Zalpha, which is specific for left-handed Z-DNA. The 2.1 angstrom crystal structure of Zalpha complexed to DNA reveals that the substrate is in the left-handed Z conformation ...

    The editing enzyme double-stranded RNA adenosine deaminase includes a DNA binding domain, Zalpha, which is specific for left-handed Z-DNA. The 2.1 angstrom crystal structure of Zalpha complexed to DNA reveals that the substrate is in the left-handed Z conformation. The contacts between Zalpha and Z-DNA are made primarily with the "zigzag" sugar-phosphate backbone, which provides a basis for the specificity for the Z conformation. A single base contact is observed to guanine in the syn conformation, characteristic of Z-DNA. Intriguingly, the helix-turn-helix motif, frequently used to recognize B-DNA, is used by Zalpha to contact Z-DNA.

    Organizational Affiliation: 

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))D [auth A],
E [auth B],
F [auth C]		81Homo sapiensMutation(s): 0 
Gene Names: ADAR, ADAR1, DSRAD, G1P1, IFI4
EC: 3.5.4.37
UniProt & NIH Common Fund Data Resources
Find proteins for P55265 (Homo sapiens)
Explore P55265 
Go to UniProtKB:  P55265
PHAROS:  P55265
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55265
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')A [auth D],
B [auth E],
C [auth F]		7N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.9α = 90
b = 85.9β = 90
c = 71.3γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model