4RKV

Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.098 
  • R-Value Work: 0.093 
  • R-Value Observed: 0.093 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr(2+) Ions.

Fyfe, A.C.Dunten, P.W.Martick, M.M.Scott, W.G.

(2015) J Mol Biol 427: 2205-2219

  • DOI: 10.1016/j.jmb.2015.03.022
  • Primary Citation of Related Structures:  
    4RJ1, 4RKV, 4RNE

  • PubMed Abstract: 
  • Guanine-rich sequences can, under appropriate conditions, adopt a distinctive, four-stranded, helical fold known as a G-quadruplex. Interest in quadruplex folds has grown in recent years as evidence of their biological relevance has accumulated from ...

    Guanine-rich sequences can, under appropriate conditions, adopt a distinctive, four-stranded, helical fold known as a G-quadruplex. Interest in quadruplex folds has grown in recent years as evidence of their biological relevance has accumulated from both sequence analysis and function-specific assays. The folds are unusually stable and their formation appears to require close management to maintain cell health; regulatory failure correlates with genomic instability and a number of cancer phenotypes. Biologically relevant quadruplex folds are anticipated to form transiently in mRNA and in single-stranded, unwound DNA. To elucidate factors, including bound solvent, that contribute to the stability of RNA quadruplexes, we examine, by X-ray crystallography and small-angle X-ray scattering, the structure of a previously reported tetramolecular quadruplex, UGGGGU stabilized by Sr(2+) ions. Crystal forms of the octameric assembly formed by this sequence exhibit unusually strong diffraction and anomalous signal enabling the construction of reliable models to a resolution of 0.88Å. The solvent structure confirms hydration patterns reported for other nucleic acid helical conformations and provides support for the greater stability of RNA quadruplexes relative to DNA. Novel features detected in the octameric RNA assembly include a new crystal form, evidence of multiple conformations and structural variations in the 3' U tetrad, including one that leads to the formation of a hydrated internal cavity.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')A, B6synthetic construct
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SR
    Query on SR

    Download CCD File 
    A, B
    STRONTIUM ION
    Sr
    PWYYWQHXAPXYMF-UHFFFAOYSA-N
     Ligand Interaction
    CA
    Query on CA

    Download CCD File 
    B
    CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N
     Ligand Interaction
    NA
    Query on NA

    Download CCD File 
    A, B
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 0.88 Å
    • R-Value Free: 0.098 
    • R-Value Work: 0.093 
    • R-Value Observed: 0.093 
    • Space Group: P 4 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 36.645α = 90
    b = 36.645β = 90
    c = 37.078γ = 90
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    PHASERphasing
    REFMACrefinement
    SCALAdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2014-11-19
      Type: Initial release
    • Version 1.1: 2015-06-24
      Changes: Database references