248D

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: 1.83 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • Primary Citation of Related Structures:  247D

  • 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 divale ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(*GP*CP*GP*)-D(*AP*TP*AP*TP*AP*)-R(*CP*GP*C)-3'), ORTHORHOMBICA11N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download SDF File 
Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.159 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 25.890α = 90.00
b = 33.970β = 90.00
c = 57.560γ = 90.00
Software Package:
Software NamePurpose
R-AXISdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model