Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.47 kDa 
• Atom Count: 2844 
• Modelled Residue Count: 133 
• Deposited Residue Count: 142 
• Unique nucleic acid chains: 1

5E54

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

• PDB DOI: 10.2210/pdb5E54/pdb
• NDB: 5E54

• Classification: RNA
• Organism(s): Vibrio vulnificus
• Mutation(s): No 


• Deposited: 2015-10-07 Released: 2016-11-23 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.256 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

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

• PubMed: 27841871 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Vibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain	A, B	71	Vibrio vulnificus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.256 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.91	α = 90
b = 46.72	β = 94.06
c = 92.25	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
Coot	model building
Cheetah	data collection
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-10-07 
• Released Date: 2016-11-23 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 1.2: 2017-10-11
  Changes: Data collection, Refinement description