1K8S

BULGED ADENOSINE IN AN RNA DUPLEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

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This is version 1.3 of the entry. See complete history


Literature

Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement.

Thiviyanathan, V.Guliaev, A.B.Leontis, N.B.Gorenstein, D.G.

(2000) J Mol Biol 300: 1143-1154

  • DOI: 10.1006/jmbi.2000.3931
  • Primary Citation of Related Structures:  
    1K8S

  • PubMed Abstract: 
  • Bulges are common structural motifs in RNA secondary structure and are thought to play important roles in RNA-protein and RNA-drug interactions. Adenosine bases are the most commonly occurring unpaired base in double helical RNA secondary structures. The solution conformation and dynamics of a 25-nucleotide RNA duplex containing an unpaired adenosine, r(GGCAGAGUGCCGC): r(GCGGCACCUGCC) have been studied by NMR spectroscopy and MORASS iterative relaxation matrix structural refinement ...

    Bulges are common structural motifs in RNA secondary structure and are thought to play important roles in RNA-protein and RNA-drug interactions. Adenosine bases are the most commonly occurring unpaired base in double helical RNA secondary structures. The solution conformation and dynamics of a 25-nucleotide RNA duplex containing an unpaired adenosine, r(GGCAGAGUGCCGC): r(GCGGCACCUGCC) have been studied by NMR spectroscopy and MORASS iterative relaxation matrix structural refinement. The results show that the bulged adenosine residue stacks into the RNA duplex with little perturbation around the bulged region. Most of the bases in the RNA duplex adopt C(3)'-endo conformation, exhibiting the N-type sugar pucker as found in the A form helices. The sugars of the bulged residue and the 5' flanking residue to it are found to exhibit C(2)'-endo conformation. None of the residues are in syn conformation.


    Organizational Affiliation

    Sealy Center for Structural Biology and Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, TX 77555-1157, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*GP*CP*AP*GP*AP*GP*UP*GP*CP*CP*GP*C)-3'A 13N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*GP*GP*CP*AP*CP*CP*UP*GP*CP*C)-3'B 12N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • OLDERADO: 1K8S Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations