3IRQ

Crystal structure of a Z-Z junction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a junction between two Z-DNA helices.

de Rosa, M.de Sanctis, D.Rosario, A.L.Archer, M.Rich, A.Athanasiadis, A.Carrondo, M.A.

(2010) Proc Natl Acad Sci U S A 107: 9088-9092

  • DOI: https://doi.org/10.1073/pnas.1003182107
  • Primary Citation of Related Structures:  
    3IRQ, 3IRR

  • PubMed Abstract: 

    The double helix of DNA, when composed of dinucleotide purine-pyrimidine repeats, can adopt a left-handed helical structure called Z-DNA. For reasons not entirely understood, such dinucleotide repeats in genomic sequences have been associated with genomic instability leading to cancer. Adoption of the left-handed conformation results in the formation of conformational junctions: A B-to-Z junction is formed at the boundaries of the helix, whereas a Z-to-Z junction is commonly formed in sequences where the dinucleotide repeat is interrupted by single base insertions or deletions that bring neighboring helices out of phase. B-Z junctions are shown to result in exposed nucleotides vulnerable to chemical or enzymatic modification. Here we describe the three-dimensional structure of a Z-Z junction stabilized by Zalpha, the Z-DNA binding domain of the RNA editing enzyme ADAR1. We show that the junction structure consists of a single base pair and leads to partial or full disruption of the helical stacking. The junction region allows intercalating agents to insert themselves into the left-handed helix, which is otherwise resistant to intercalation. However, unlike a B-Z junction, in this structure the bases are not fully extruded, and the stacking between the two left-handed helices is not continuous.


  • Organizational Affiliation

    Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6 P-2780-156 Oeiras, Portugal.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Double-stranded RNA-specific adenosine deaminaseA [auth D],
D [auth C],
E [auth B],
F [auth A]
67Homo sapiensMutation(s): 0 
Gene Names: ADARADAR1DSRADG1P1IFI4
EC: 3.5.4
UniProt & NIH Common Fund Data Resources
Find proteins for P55265 (Homo sapiens)
Explore P55265 
Go to UniProtKB:  P55265
PHAROS:  P55265
GTEx:  ENSG00000160710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55265
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*TP*CP*GP*CP*GP*CP*G)-3')B [auth G]15N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*CP*CP*GP*CP*GP*CP*GP*AP*CP*GP*CP*GP*CP*G)-3')C [auth F]15N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.283α = 90
b = 99.761β = 90
c = 106.482γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Refinement description