1QBJ

CRYSTAL STRUCTURE OF THE ZALPHA Z-DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1QBJ/pdb
• NAKB: 1QBJ

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


• Deposited: 1999-04-22 Released: 1999-07-02 
• Deposition Author(s): Schwartz, T., Rould, M.A., Rich, A.

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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 

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

• PubMed: 10364558 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.35 kDa 
• Atom Count: 2,142 
• Modelled Residue Count: 212 
• Deposited Residue Count: 264 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DOUBLE-STRANDED RNA SPECIFIC ADENOSINE DEAMINASE (ADAR1))	D [auth A], E [auth B], F [auth C]	81	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000160710

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')	A [auth D], B [auth E], C [auth F]	7	N/A

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 = 85.9	α = 90
b = 85.9	β = 90
c = 71.3	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-07-02 
Deposition Author(s): Schwartz, T., Rould, M.A., Rich, A.

Revision History  

• 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
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references