1F1T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
MALACHITE GREEN APTAMER RNAA38N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ROS
Query on ROS

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Download CCD File 
A
N,N'-TETRAMETHYL-ROSAMINE
(6-DIMETHYLAMINO-9-PHENYL-XANTHEN-3-YLIDENE)-DIMETHYL-AMMONIUM
C23 H23 N2 O
NGSXFKKYKWBNPO-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

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Download CCD File 
A
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BU
Query on 5BU
A
RNA LINKINGC9 H12 Br N2 O9 PU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ROSKd: 40 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.261 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 55.297α = 90.00
b = 55.297β = 90.00
c = 143.920γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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