4U92

Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad.

Zhang, D.Huang, T.Lukeman, P.S.Paukstelis, P.J.

(2014) Nucleic Acids Res. 42: 13422-13429

  • DOI: 10.1093/nar/gku1122

  • PubMed Abstract: 
  • We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged ...

    We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation.


    Organizational Affiliation

    Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA paukstel@umd.edu.,Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA.,Chemistry and Biochemistry Department, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768, USA.,Chemistry Department, St. John's University, 8000 Utopia Parkway, Queens, NY 11439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*AP*KP*GP*CP*GP*TP*GP*G)-3')A,B10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BA
Query on BA

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Download CCD File 
A, B
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CNV
Query on CNV
A, B
non-polymerC3 H5 N

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.129 
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 29.621α = 90.00
b = 29.621β = 90.00
c = 63.737γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Database references