1RAW

ATP BINDING RNA APTAMER IN COMPLEX WITH AMP, NMR, 10 STRUCTURES

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 1996-07-17 Released: 1997-01-27 
  • Deposition Author(s): Dieckmann, T., Feigon, J.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST ENERGY STRUCTURES 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Solution Structure of an ATP-Binding RNA Aptamer Reveals a Novel Fold

Dieckmann, T., Suzuki, E., Nakamura, G.K., Feigon, J.

(1996) RNA 2: 628-640

  • Primary Citation of Related Structures:  
    1RAW

  • PubMed Abstract: 

    • In vitro selection has been used to isolate several RNA aptamers that bind specifically to biological cofactors. A well-characterized example in the ATP-binding RNA aptamer family, which contains a conserved 11-base loop opposite a bulged G and flanked by regions of double-stranded RNA ...

    In vitro selection has been used to isolate several RNA aptamers that bind specifically to biological cofactors. A well-characterized example in the ATP-binding RNA aptamer family, which contains a conserved 11-base loop opposite a bulged G and flanked by regions of double-stranded RNA. The nucleotides in the consensus sequence provide a binding pocket for ATP (or AMP), which binds with a Kd in the micromolar range. Here we present the three-dimensional solution structure of a 36-nucleotide ATP-binding RNA aptamer complexed with AMP, determined from NMR-derived distance and dihedral angle restraints. The conserved loop and bulged G form a novel compact, folded structure around the AMP. The backbone tracing of the loop nucleotides can be described by a Greek zeta (zeta). Consecutive loop nucleotides G, A, A form a U-turn at the bottom of the zeta, and interact with the AMP to form a structure similar to a GNRA tetraloop, with AMP standing in for the final A. Two asymmetric G. G base pairs close the stems flanking the internal loop. Mutated aptamers support the existence of the tertiary interactions within the consensus nucleotides and with the AMP found in the calculated structures.

    Related Citations: 
    • An RNA Motif that Binds ATP
      Sassanfar, M., Szostak, J.W.
      (1993) Nature 364: 550
    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.



Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA APTAMERA 36N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP
Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: LOWEST ENERGY STRUCTURES 
  • OLDERADO: 1RAW Olderado

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-27
    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: 2022-03-02
    Changes: Database references, Derived calculations, Other