2GRB

Crystal Structure of an RNA Quadruplex Containing Inosine-tetrad


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads.

Pan, B.Shi, K.Sundaralingam, M.

(2006) J.Mol.Biol. 363: 451-459

  • DOI: 10.1016/j.jmb.2006.08.022

  • PubMed Abstract: 
  • Polyinosinic acid has been known to adopt the four-stranded helical structure but its basic unit, inosine tetrad (I tetrad), has not been determined at the atomic level. Here we report the crystal structure of an RNA quadruplex containing an I tetrad ...

    Polyinosinic acid has been known to adopt the four-stranded helical structure but its basic unit, inosine tetrad (I tetrad), has not been determined at the atomic level. Here we report the crystal structure of an RNA quadruplex containing an I tetrad at 1.4 A resolution. The I tetrad has one cyclic hydrogen bond N1...O6 with the bond length of 2.7 A. A water bridge is observed in the minor groove side of the base tetrad. Even though it is sandwiched by guanine tetrads (G tetrads), the I tetrad is buckled towards the 3' side of the tetrad plane, which results from the different interaction strength with K ions on two sides of the tetrad plane. Comparison with both G tetrad and adenine tetrad indicates that lack of NH2 in the C2 position makes the I tetrad prone to buckle for interactions with ligands. Two U*(G-G-G-G) base pentads are observed at the junction of the 5' termini of two quadruplexes. The uridine residue in the base pentad is engaged in two hydrogen bonding interactions (N2(G)-H...O2(U) and O2'(G)-H...O4(U)) and a water-mediated interaction (N3(G) and N3(U)) with the G tetrad. We also discuss the roles of amino group in purine tetrads and the inter-quadruplex interactions in RNA molecules. These quadruplexes may interact with each other by stacking, groove binding and intercalation.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. baocheng.pan@yale.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*(U33)P*GP*IP*GP*GP*U)-3'A,B,C,D,E,F,G,H6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, D, E, F, H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

Download SDF File 
Download CCD File 
B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
U33
Query on U33
A, B, C, D, E, F, G, H
DNA LINKINGC9 H11 Br N2 O5DU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 29.060α = 90.00
b = 52.738β = 102.98
c = 37.344γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
ADSCdata collection
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance