5ZUP

Crystal Structure of BZ junction in diverse sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

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This is version 1.3 of the entry. See complete history


Literature

Sequence preference and structural heterogeneity of BZ junctions.

Kim, D.Hur, J.Han, J.H.Ha, S.C.Shin, D.Lee, S.Park, S.Sugiyama, H.Kim, K.K.

(2018) Nucleic Acids Res 46: 10504-10513

  • DOI: https://doi.org/10.1093/nar/gky784
  • Primary Citation of Related Structures:  
    5ZU1, 5ZUO, 5ZUP

  • PubMed Abstract: 

    BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We determined three crystal structures of BZ junctions with diverse sequences followed by spectroscopic validation of DNA conformation. The structural features of the BZ junctions were well conserved regardless of sequences via the continuous base stacking through B-to-Z DNA with A-T base extrusion. However, the sequence-dependent structural heterogeneity of the junctions was also observed in base step parameters that are correlated with steric constraints imposed during Z-DNA formation. Further, circular dichroism and fluorescence-based analysis of BZ junctions revealed that a base extrusion was only found at the A-T base pair present next to a stable dinucleotide Z-DNA unit. Our findings suggest that Z-DNA formation in the genome is influenced by the sequence preference for BZ junctions.


  • Organizational Affiliation

    Department of Molecular Cell Biology, Institute for Antimicrobial Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Korea.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Double-stranded RNA-specific adenosine deaminase
A, B, C, D
67Homo sapiensMutation(s): 0 
Gene Names: ADARADAR1DSRADG1P1IFI4
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 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
(5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*AP*AP*TP*AP*AP*AP*CP*C)-3')17synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
(5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*CP*GP*CP*GP*CP*GP*CP*G)-3')17synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.605α = 90
b = 112.605β = 90
c = 61.833γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Korea, Republic OfSSTF-BA1301-01

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references