5E54

Two apo structures of the adenine riboswitch aptamer domain determined using an X-ray free electron laser

Summary for 5E54

• Entry DOI: 10.2210/pdb5e54/pdb
• Descriptor: Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain, MAGNESIUM ION (3 entities in total)
• Functional Keywords: adenine riboswitch, purine riboswitch, apo, ligand-free, rna, gene regulation, x-ray free electron laser
• Biological source: Vibrio vulnificus
• Total number of polymer chains: 2
• Total formula weight: 45471.99

Authors

Stagno, J.R.,Wang, Y.-X.,Liu, Y.,Bhandari, Y.R.,Conrad, C.E.,Nelson, G.,Li, C.,Wendel, D.R.,White, T.A.,Barty, A.,Tuckey, R.A.,Zatsepin, N.A.,Grant, T.D.,Fromme, P.,Tan, K.,Ji, X.,Spence, J.C.H. (deposition date: 2015-10-07, release date: 2016-11-23, Last modification date: 2023-08-30)

Primary citation

Stagno, J.R.,Liu, Y.,Bhandari, Y.R.,Conrad, C.E.,Panja, S.,Swain, M.,Fan, L.,Nelson, G.,Li, C.,Wendel, D.R.,White, T.A.,Coe, J.D.,Wiedorn, M.O.,Knoska, J.,Oberthuer, D.,Tuckey, R.A.,Yu, P.,Dyba, M.,Tarasov, S.G.,Weierstall, U.,Grant, T.D.,Schwieters, C.D.,Zhang, J.,Ferre-D'Amare, A.R.,Fromme, P.,Draper, D.E.,Liang, M.,Hunter, M.S.,Boutet, S.,Tan, K.,Zuo, X.,Ji, X.,Barty, A.,Zatsepin, N.A.,Chapman, H.N.,Spence, J.C.,Woodson, S.A.,Wang, Y.X.
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.
Nature, 541:242-246, 2017

PubMed 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.

PubMed: 27841871
DOI: 10.1038/nature20599

Experimental method

X-RAY DIFFRACTION (2.3 Å)