1P79

Crystal structure of a bulged RNA tetraplex: implications for a novel binding site in RNA tetraplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Bulged RNA Tetraplex at 1.1 A Resolution: Implications for a Novel Binding Site in RNA Tetraplex

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

(2003) STRUCTURE 11: 1423-1430


  • PubMed Abstract: 
  • Bulges are an important structural motif in RNA and can be used as recognition and interaction sites in RNA-protein interaction and RNA-RNA interaction. Here we report the first crystal structure of a bulged RNA tetraplex at 1.1 A resolution. The hex ...

    Bulges are an important structural motif in RNA and can be used as recognition and interaction sites in RNA-protein interaction and RNA-RNA interaction. Here we report the first crystal structure of a bulged RNA tetraplex at 1.1 A resolution. The hexamer r(U)(BrdG)r(UGGU) forms a parallel tetraplex with the uridine sandwiched by guanines bulging out. The bulged uridine adopts the syn glycosidic conformation and its O2 and N3 atoms face outwards, serving as an effective recognition and interaction site. The bulge formation both widens the groove width and changes the groove hydrogen-bonding pattern on its 5' side. However, the bulge does not make any bends or kinks in the tetraplex structure. The present study demonstrates the dramatic difference between uridine and guanine in forming tetraplex structure. In addition, both G(syn) tetrad and G(anti) tetrad have been observed. They display the same base-pairing pattern and similar C1'-C1' distance but different hydrogen-bonding patterns in the groove.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Lab, 176 West 19th Avenue, Columbus, OH, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*UP*GP*UP*GP*GP*U)-3'A6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.127 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 35.014α = 90.00
b = 35.014β = 90.00
c = 22.257γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance