2GXB

Crystal Structure of The Za Domain bound to Z-RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Left-Handed RNA Double Helix Bound by the Zalpha Domain of the RNA-Editing Enzyme ADAR1.

Placido, D.Brown, B.A.Lowenhaupt, K.Rich, A.Athanasiadis, A.

(2007) Structure 15: 395-404

  • DOI: 10.1016/j.str.2007.03.001

  • PubMed Abstract: 
  • The A form RNA double helix can be transformed to a left-handed helix, called Z-RNA. Currently, little is known about the detailed structural features of Z-RNA or its involvement in cellular processes. The discovery that certain interferon-response p ...

    The A form RNA double helix can be transformed to a left-handed helix, called Z-RNA. Currently, little is known about the detailed structural features of Z-RNA or its involvement in cellular processes. The discovery that certain interferon-response proteins have domains that can stabilize Z-RNA as well as Z-DNA opens the way for the study of Z-RNA. Here, we present the 2.25 A crystal structure of the Zalpha domain of the RNA-editing enzyme ADAR1 (double-stranded RNA adenosine deaminase) complexed to a dUr(CG)(3) duplex RNA. The Z-RNA helix is associated with a unique solvent pattern that distinguishes it from the otherwise similar conformation of Z-DNA. Based on the structure, we propose a model suggesting how differences in solvation lead to two types of Z-RNA structures. The interaction of Zalpha with Z-RNA demonstrates how the interferon-induced isoform of ADAR1 could be targeted toward selected dsRNAs containing purine-pyrimidine repeats, possibly of viral origin.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Double-stranded RNA-specific adenosine deaminase
A, B
66Homo 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: 1
MoleculeChainsLengthOrganism
5'-R(P*(DU)P*CP*GP*CP*GP*CP*G)-3'E,F7N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B, E, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.603α = 90.00
b = 92.776β = 90.00
c = 50.229γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
EPMRphasing
SCALAdata scaling
CCP4data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance