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: 2.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.186 
  • R-Value Observed: 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.

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

(1996) Proc Natl Acad Sci U S A 93: 12851-12855

  • DOI: 10.1073/pnas.93.23.12851
  • Primary Citation of Related Structures:  
    283D

  • 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 base pairs make up an internal loop in the middle of the duplex, including sheared G ...

    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

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*C)-3')A 12N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.71α = 90
b = 37.71β = 90
c = 88.3γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
R-AXISdata reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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