1F1T

CRYSTAL STRUCTURE OF THE MALACHITE GREEN APTAMER COMPLEXED WITH TETRAMETHYL-ROSAMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

2.8 A crystal structure of the malachite green aptamer.

Baugh, C.Grate, D.Wilson, C.

(2000) J Mol Biol 301: 117-128

  • DOI: 10.1006/jmbi.2000.3951
  • Primary Citation of Related Structures:  
    1F1T

  • PubMed Abstract: 
  • Previous in vitro selection experiments identified an RNA aptamer that recognizes the chromophore malachite green (MG) with a high level of affinity, and which undergoes site-specific cleavage following laser irradiation. To understand the mechanism by w ...

    Previous in vitro selection experiments identified an RNA aptamer that recognizes the chromophore malachite green (MG) with a high level of affinity, and which undergoes site-specific cleavage following laser irradiation. To understand the mechanism by which this RNA folds to recognize specifically its ligand and the structural basis for chromophore-assisted laser inactivation, we have determined the 2.8 A crystal structure of the aptamer bound to tetramethylrosamine (TMR), a high-affinity MG analog. The ligand-binding site is defined by an asymmetric internal loop, flanked by a pair of helices. A U-turn and several non-canonical base interactions stabilize the folding of loop nucleotides around the TMR. The aptamer utilizes several tiers of stacked nucleotides arranged in pairs, triples, and a novel base quadruple to effectively encapsulate the ligand. Even in the absence of specific stabilizing hydrogen bonds, discrimination between related fluorophores and chromophores is possible due to tight packing in the RNA binding pocket, which severely limits the size and shape of recognized ligands. The site of laser-induced cleavage lies relatively far from the bound TMR ( approximately 15 A). The unusual backbone conformation of the cleavage site nucleotide and its high level of solvent accessibility may combine to allow preferential reaction with freely diffusing hydroxyl radicals generated at the bound ligand. Several observations, however, favor alternative mechanisms for cleavage, such as conformational changes in the aptamer or long-range electron transfer between the bound ligand and the cleavage site nucleotide.


    Organizational Affiliation

    Department of Biology and Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
MALACHITE GREEN APTAMER RNAA38N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.297α = 90
b = 55.297β = 90
c = 143.92γ = 120
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance