247D

CRYSTAL STRUCTURES OF AN A-FORM DUPLEX WITH SINGLE-ADENOSINE BULGES AND A CONFORMATIONAL BASIS FOR SITE SPECIFIC RNA SELF-CLEAVAGE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage.

Portmann, S.Grimm, S.Workman, C.Usman, N.Egli, M.

(1996) Chem Biol 3: 173-184

  • DOI: https://doi.org/10.1016/s1074-5521(96)90260-4
  • Primary Citation of Related Structures:  
    247D, 248D

  • PubMed Abstract: 

    Bulged nucleotides are common secondary structural motifs in RNA molecules and are often involved in RNA-RNA and RNA-protein interactions. RNA is selectively cleaved at bulge sites (when compared to other sites within stems) in the presence of divalent metal cations. The effects of bulge nucleotides on duplex stability and topology have been extensively investigated, but no detailed X-ray structures of bulge-containing RNA fragments have been available.


  • Organizational Affiliation

    Department of Molecular Pharmacology & Biological Chemistry, Northwestern University Medical School, 303 East Chicago Avenue, Chicago, IL 60611-3008, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA/RNA (5'-R(*GP*CP*GP*)-D(*AP*TP*AP*TP*AP*)-R(*CP*GP*C)-3')11N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.245α = 90
b = 27.245β = 90
c = 177.399γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
R-AXISdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2024-02-14
    Changes: Atomic model, Data collection, Database references