2AU4

Class I GTP aptamer

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 1 

wwPDB Validation   3D Report Full Report


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


Literature

Solution structure of an informationally complex high-affinity RNA aptamer to GTP.

Carothers, J.M., Davis, J.H., Chou, J.J., Szostak, J.W.

(2006) RNA 12: 567-579

  • DOI: 10.1261/rna.2251306
  • Primary Citation of Related Structures:  
    2AU4

  • PubMed Abstract: 

    • Higher-affinity RNA aptamers to GTP are more informationally complex than lower-affinity aptamers. Analog binding studies have shown that the additional information needed to improve affinity does not specify more interactions with the ligand. In light of those observations, we would like to understand the structural characteristics that enable complex aptamers to bind their ligands with higher affinity ...

    Higher-affinity RNA aptamers to GTP are more informationally complex than lower-affinity aptamers. Analog binding studies have shown that the additional information needed to improve affinity does not specify more interactions with the ligand. In light of those observations, we would like to understand the structural characteristics that enable complex aptamers to bind their ligands with higher affinity. Here we present the solution structure of the 41-nt Class I GTP aptamer (K(d) = 75 nM) as determined by NMR. The backbone of the aptamer forms a reverse-S that shapes the binding pocket. The ligand nucleobase stacks between purine platforms and makes hydrogen bonds with the edge of another base. Interestingly, the local modes of interaction for the Class I aptamer and an RNA aptamer that binds ATP with a K(d) of 6 microM are very much alike. The aptamers exhibit nearly identical levels of binding specificity and fraction of ligand sequestered from the solvent (81%-85%). However, the GTP aptamer is more informationally complex (approximately 45 vs. 35 bits) and has a larger recognition bulge (15 vs. 12 nucleotides) with many more stabilizing base-base interactions. Because the aptamers have similar modes of ligand binding, we conclude that the stabilizing structural elements in the Class I aptamer are responsible for much of the difference in K(d). These results are consistent with the hypothesis that increasing the number of intra-RNA interactions, rather than adding specific contacts to the ligand, is the simplest way to improve binding affinity.

    Organizational Affiliation: 

    Department of Molecular Biology and Center for Computational and Integrative Biology, Simches Research Center 7215, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Class I RNA aptamer to GTPA 41N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GTP PDBBind:  2AU4 Kd: 75 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 1 
  • OLDERADO: 2AU4 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-09
    Changes: Data collection, Database references, Derived calculations