Macromolecule Content

• Total Structure Weight: 12022.23 
• Atom Count: 796 
• Residue Count: 36 
• Unique nucleic acid chains: 1

1RAW

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

• DOI: 10.2210/pdb1RAW/pdb
• NDB: 1RAW

• Classification: RNA


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

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Experimental Data Snapshot

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

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

• PubMed: 8756406 


• 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. 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.

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Related Citations: 

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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
RNA APTAMER	A	36	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
AMP	A	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

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

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	model building
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History 

• Version 1.0: 1997-01-27
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance