5ZUP

Crystal Structure of BZ junction in diverse sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.1 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. --: --

  • DOI: 10.1093/nar/gky784
  • Primary Citation of Related Structures:  

  • 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 s ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Double-stranded RNA-specific adenosine deaminase
A, B, C, D
67Homo sapiensMutation(s): 0 
Gene Names: ADAR (ADAR1, DSRAD, G1P1, IFI4)
EC: 3.5.4.37
Find proteins for P55265 (Homo sapiens)
Go to Gene View: ADAR
Go to UniProtKB:  P55265
Entity ID: 2
MoleculeChainsLengthOrganism
(5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*AP*AP*TP*AP*AP*AP*CP*C)-3')E17synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
(5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*CP*GP*CP*GP*CP*GP*CP*G)-3')F17synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.258 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 112.605α = 90.00
b = 112.605β = 90.00
c = 61.833γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-05-08 
  • Released Date: 2018-08-29 
  • Deposition Author(s): Kim, K.K., Kim, D.

Funding OrganizationLocationGrant Number
Korea, Republic OfSSTF-BA1301-01

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references