Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.36 kDa 
• Atom Count: 793 
• Modelled Residue Count: 79 
• Deposited Residue Count: 79 
• Unique protein chains: 1

1XMK

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

• PDB DOI: 10.2210/pdb1XMK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-10-03 Released: 2005-08-02 
• Deposition Author(s): Athanasiadis, A., Placido, D., Maas, S., Brown II, B.A., Lowenhaupt, K., Rich, A.

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Experimental Data Snapshot

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

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

• PubMed: 16023667 
• 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. 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.

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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

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Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-stranded RNA-specific adenosine deaminase	A	79	Homo sapiens	Mutation(s): 0  Gene Names: ADAR, ADAR1, DSRAD, IFI4, G1P1 EC: 3.5.4 (PDB Primary Data), 3.5.4.37 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P55265 (Homo sapiens) Explore P55265  Go to UniProtKB:  P55265
PHAROS:  P55265

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
NI	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 35.557	α = 90
b = 43.526	β = 90
c = 45.471	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing
SHELXL	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-03 
• Released Date: 2005-08-02 
Deposition Author(s): Athanasiadis, A., Placido, D., Maas, S., Brown II, B.A., Lowenhaupt, K., Rich, A.

Revision History  

• 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