1XMK

The Crystal structure of the Zb domain from the RNA editing enzyme ADAR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.183 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Crystal Structure of the Z[beta] Domain of the RNA-editing Enzyme ADAR1 Reveals Distinct Conserved Surfaces Among Z-domains.

Athanasiadis, A.Placido, D.Maas, S.Brown II, B.A.Lowenhaupt, K.Rich, A.

(2005) J Mol Biol 351: 496-507

  • DOI: 10.1016/j.jmb.2005.06.028
  • Primary Citation of Related Structures:  
    1XMK

  • PubMed Abstract: 
  • The Zalpha domains represent a growing subfamily of the winged helix-turn-helix (HTH) domain family whose members share a remarkable ability to bind specifically to Z-DNA and/or Z-RNA. They have been found exclusively in proteins involved in interferon response and, while their importance in determining pox viral pathogenicity has been demonstrated, their actual target and biological role remain obscure ...

    The Zalpha domains represent a growing subfamily of the winged helix-turn-helix (HTH) domain family whose members share a remarkable ability to bind specifically to Z-DNA and/or Z-RNA. They have been found exclusively in proteins involved in interferon response and, while their importance in determining pox viral pathogenicity has been demonstrated, their actual target and biological role remain obscure. Cellular proteins containing Zalpha domains bear a second homologous domain termed Zbeta, which appears to lack the ability to bind left-handed nucleic acids. Here, we present the crystal structure of the Zbeta domain from the human double-stranded RNA adenosine deaminase ADAR1 at 0.97 A, determined by single isomorphous replacement including anomalous scattering. Zbeta maintains a winged-HTH fold with the addition of a C-terminal helix. Mapping of the Zbeta conservation profile on the Zbeta surface reveals a new conserved surface formed partly by the terminal helix 4, involved in metal binding and dimerization and absent from Zalpha domains. Our results show how two domains similar in fold may have evolved into different functional entities even in the context of the same protein.


    Related Citations: 
    • Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins
      Schwartz, T., Behlke, J., Lowenhaupt, K., Heinemann, U., Rich, A.
      (2001) Nat Struct Mol Biol 8: 761
    • 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

    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. alekosathanasiadis@hotmail.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Double-stranded RNA-specific adenosine deaminaseA79Homo sapiensMutation(s): 0 
Gene Names: ADARADAR1DSRADIFI4G1P1
EC: 3.5.4 (PDB Primary Data), 3.5.4.37 (UniProt)
Find proteins for P55265 (Homo sapiens)
Explore P55265 
Go to UniProtKB:  P55265
NIH Common Fund Data Resources
PHAROS:  P55265
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
D [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.183 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.557α = 90
b = 43.526β = 90
c = 45.471γ = 90
Software Package:
Software NamePurpose
SHELXrefinement
MOSFLMdata reduction
CCP4data scaling
SHARPphasing
SHELXLrefinement

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: 2018-01-24
    Changes: Database references