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

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.379 
  • R-Value Work: 0.349 
  • R-Value Observed: 0.350 

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Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.

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.

(2017) Nature 541: 242-246

  • DOI: https://doi.org/10.1038/nature20599
  • Primary Citation of Related Structures:  
    5E54, 5SWD, 5SWE

  • 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.

  • Organizational Affiliation

    Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA.

Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domainA [auth X]71Vibrio vulnificus
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADE

Download Ideal Coordinates CCD File 
C5 H5 N5
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.379 
  • R-Value Work: 0.349 
  • R-Value Observed: 0.350 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.9α = 90
b = 154.9β = 90
c = 25.2γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Data collection, Database references
  • Version 1.2: 2017-10-11
    Changes: Data collection
  • Version 1.3: 2018-02-14
    Changes: Data collection
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2023-10-04
    Changes: Refinement description