5SWE : Ligand-bound structure of adenine riboswitch aptamer domain converted in crystal from its ligand-free state using ligand mixing serial femtosecond crystallography

  • X. Ji (Contributor)
  • Thomas Grant (Contributor)
  • Y. Liu (Contributor)
  • J. R. Stagno (Contributor)
  • R. A. Tuckey (Contributor)
  • Thomas A. White (Contributor)
  • Petra Fromme (Contributor)
  • Chufeng Li (Contributor)
  • Anton Barty (Contributor)
  • Y. R. Bhandari (Contributor)
  • Chelsie E. Conrad (Contributor)
  • G. Nelson (Contributor)
  • J.C.H. Spence (Arizona State University) (Contributor)
  • D. R. Wendel (Contributor)
  • N.A. Zatsepin (Arizona State University) (Contributor)
  • Y. X. Wang (Contributor)

Dataset

Description

Experimental Technique/Method:X-RAY DIFFRACTION
Resolution:3.0
Classification:RNA
Release Date:2016-11-23
Deposition Date:2016-08-08
Revision Date:2017-01-25#2017-10-11#2018-02-14
Molecular Weight:22822.51
Macromolecule Type:RNA
Residue Count:71
Atom Site Count:1512
DOI:10.2210/pdb5swe/pdb

Abstract:
Riboswitches are structural RNA elements that are generally located in the 5' untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of 'mix-and-inject' time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.
Date made availableNov 23 2016
PublisherRCSB-PDB

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