Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.68 kDa 
• Atom Count: 2,579 
• Modelled Residue Count: 281 
• Deposited Residue Count: 298 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 2ACJ

Crystal structure of the B/Z junction containing DNA bound to Z-DNA binding proteins

• PDB DOI: 10.2210/pdb2ACJ/pdb
• NDB: PD0693

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


• Deposited: 2005-07-19 Released: 2005-10-25 
• Deposition Author(s): Ha, S.C., Lowenhaupt, K., Rich, A., Kim, Y.-G., Kim, K.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.285 
• R-Value Work: 0.238 
• R-Value Observed: 0.243 

Literature

Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases.

Ha, S.C., Lowenhaupt, K., Rich, A., Kim, Y.G., Kim, K.K.

(2005) Nature 437: 1183-1186

• PubMed: 16237447 
• DOI: 10.1038/nature04088
• Primary Citation of Related Structures:  
  2ACJ


• PubMed Abstract: 
  

Left-handed Z-DNA is a higher-energy form of the double helix, stabilized by negative supercoiling generated by transcription or unwrapping nucleosomes. Regions near the transcription start site frequently contain sequence motifs favourable for forming Z-DNA, and formation of Z-DNA near the promoter region stimulates transcription. Z-DNA is also stabilized by specific protein binding; several proteins have been identified with low nanomolar binding constants. Z-DNA occurs in a dynamic state, forming as a result of physiological processes then relaxing to the right-handed B-DNA. Each time a DNA segment turns into Z-DNA, two B-Z junctions form. These have been examined extensively, but their structure was unknown. Here we describe the structure of a B-Z junction as revealed by X-ray crystallography at 2.6 A resolution. A 15-base-pair segment of DNA is stabilized at one end in the Z conformation by Z-DNA binding proteins, while the other end remains B-DNA. Continuous stacking of bases between B-DNA and Z-DNA segments is found, with the breaking of one base pair at the junction and extrusion of the bases on each side (Fig. 1). These extruded bases may be sites for DNA modification.

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Organizational Affiliation: 

Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-stranded RNA-specific adenosine deaminase	C [auth A], D [auth B], E [auth C], F [auth D]	66	Homo sapiens	Mutation(s): 0  Gene Names: ADAR1, ADAR, DSRAD, G1P1, IFI4 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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*CP*AP*TP*AP*AP*AP*CP*C)-3'	A [auth E]	17	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*GP*GP*CP*GP*CP*GP*CP*G)-3'	B [auth F]	17	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.285 
• R-Value Work: 0.238 
• R-Value Observed: 0.243 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.765	α = 90
b = 110.765	β = 90
c = 61.762	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-25 
Deposition Author(s): Ha, S.C., Lowenhaupt, K., Rich, A., Kim, Y.-G., Kim, K.K.

Revision History  

• Version 1.0: 2005-10-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance