283D

A CURVED RNA HELIX INCORPORATING AN INTERNAL LOOP WITH G-A AND A-A NON-WATSON-CRICK BASE PAIRING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing.

De Bondt, H.L.Pardi, A.Holbrook, S.R.Baeyens, K.J.

(1996) Proc.Natl.Acad.Sci.USA 93: 12851-12855


  • PubMed Abstract: 
  • The crystal structure of the RNA dodecamer 5'-GGCC(GAAA)GGCC-3' has been determined from x-ray diffraction data to 2.3-A resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson-Crick b ...

    The crystal structure of the RNA dodecamer 5'-GGCC(GAAA)GGCC-3' has been determined from x-ray diffraction data to 2.3-A resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson-Crick base pairs make up an internal loop in the middle of the duplex, including sheared G.A pairs and novel asymmetric A.A pairs. This internal loop sequence produces a significant curvature and narrowing of the double helix. The helix is curved by 34 degrees from end to end and the diameter is narrowed by 24% in the internal loop. A Mn2+ ion is bound directly to the N7 of the first guanine in the Watson-Crick region following the internal loop and the phosphate of the preceding residue. This Mn2+ location corresponds to a metal binding site observed in the hammerhead catalytic RNA.


    Organizational Affiliation

    Structural Biology Division, Lawrence Berkeley National Laboratory, University of California, Berkeley 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*C)-3')A12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.186 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 37.710α = 90.00
b = 37.710β = 90.00
c = 88.300γ = 120.00
Software Package:
Software NamePurpose
R-AXISdata reduction
X-PLORrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-09-30
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance