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 

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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:  

  • 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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')A,B6synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

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Download CCD File 
A, B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-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 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 36.645α = 90.00
b = 36.645β = 90.00
c = 37.078γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PHASERphasing
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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