1KOD

RNA APTAMER COMPLEXED WITH CITRULLINE, NMR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy.

Yang, Y.Kochoyan, M.Burgstaller, P.Westhof, E.Famulok, M.

(1996) Science 272: 1343-1347

  • DOI: 10.1126/science.272.5266.1343
  • Primary Citation of Related Structures:  
    1KOC, 1KOD

  • PubMed Abstract: 
  • In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy ...

    In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.


    Related Citations: 
    • Structural Probing and Damage Selection of Citrulline-and Arginine-Specific RNA Aptamers Identify Base Positions Required for Binding
      Burgstaller, P., Kochoyan, M., Famulok, M.
      (1995) Nucleic Acids Res 23: 4769

    Organizational Affiliation

    Centre de Biochimie Structurale (CBS), Unité Mixte de Recherche, CNRS 9955, Montpellier, France.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*GP*AP*AP*GP*GP*AP*GP*UP*GP*U)-3')A 11N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*CP*GP*GP*UP*UP*AP*GP*GP*UP*CP*GP*CP*U)-3')B 14N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIR
Query on CIR

Download Ideal Coordinates CCD File 
C [auth B]CITRULLINE
C6 H13 N3 O3
RHGKLRLOHDJJDR-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Database references, Derived calculations, Other