1YFV

STRUCTURE OF (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')2 BY 2-D NMR, 1 STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 11 
  • Conformers Submitted: 
  • Selection Criteria: PUBLISHED STRUCTURE GIVEN 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics.

SantaLucia Jr., J.Turner, D.H.

(1993) Biochemistry 32: 12612-12623


  • PubMed Abstract: 
  • The duplex (rGGCGAGCC)2 contains tandem G x A mismatches--a common motif in the secondary structures of biological RNAs. The three-dimensional structure of (rGGCGAGCC)2 was derived using molecular dynamics and energy minimization with NMR-derived res ...

    The duplex (rGGCGAGCC)2 contains tandem G x A mismatches--a common motif in the secondary structures of biological RNAs. The three-dimensional structure of (rGGCGAGCC)2 was derived using molecular dynamics and energy minimization with NMR-derived restraints for 78 interproton distances (per strand), 18 hydrogen bonds for the six Watson-Crick G x C pairs, and 26 dihedral angles (per strand). The G x A mismatch structures are similar to those observed in a DNA duplex [Li, Y., Zon, G., & Wilson, W. D. (1991) Proc. Natl. Acad. Sci. U.S.A. 80, 26-30] and an RNA hairpin [Heus, H. A., & Pardi, A. (1991) Science 253, 191-193], with hydrogen bonds from guanine 2-amino and N3 to adenine N7 and 6-amino, respectively. The other G 2-amino and A 6-amino protons are within hydrogen-bonding distance of a phosphate oxygen and 2'-oxygen, respectively. Strong interstrand A-A and G-G stacking is observed between the G x A mismatches. This contrasts with the poor stacking observed between the G x A mismatches and closing G x C base pairs. The stems are basically A-form with all bases in the anti conformation and all nonterminal sugars in the C3'-endo conformation. The structure rationalizes previous thermodynamic, circular dichroism, and imino proton NMR results and suggests tandem G x A mismatches in RNA may provide a contact site for tertiary interactions.


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley 94720.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(GP*GP*CP*GP*AP*GP*CP*C)-3')A,B8N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 11 
  • Conformers Submitted: 
  • Selection Criteria: PUBLISHED STRUCTURE GIVEN 
Software Package:
Software NamePurpose
X-PLORphasing
VNMRphasing
X-PLORrefinement
X-PLORmodel building
VNMRmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance