6VWV | pdb_00006vwv

Transitional unit cell 2 of adenine riboswitch aptamer crystal phase transition upon ligand binding

• PDB DOI: https://doi.org/10.2210/pdb6VWV/pdb
• NAKB: 6VWV

• Classification: RNA
• Organism(s): Vibrio vulnificus
• Mutation(s): Yes 


• Deposited: 2020-02-20 Released: 2020-11-11 
• Deposition Author(s): Stagno, J.R., Wang, Y.-X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.279 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Synchronous RNA conformational changes trigger ordered phase transitions in crystals.

Ramakrishnan, S., Stagno, J.R., Conrad, C.E., Ding, J., Yu, P., Bhandari, Y.R., Lee, Y.T., Pauly, G., Yefanov, O., Wiedorn, M.O., Knoska, J., Oberthur, D., White, T.A., Barty, A., Mariani, V., Li, C., Brehm, W., Heinz, W.F., Magidson, V., Lockett, S., Hunter, M.S., Boutet, S., Zatsepin, N.A., Zuo, X., Grant, T.D., Pandey, S., Schmidt, M., Spence, J.C.H., Chapman, H.N., Wang, Y.X.

(2021) Nat Commun 12: 1762-1762

• PubMed: 33741910 
• DOI: https://doi.org/10.1038/s41467-021-21838-5
• Primary Citation Related Structures: 
  6VWT, 6VWV


• PubMed Abstract: 
  

  Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.

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Organizational Affiliation: 
• Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.
Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
Department of Physics, Universität Hamburg, Hamburg, Germany.
Department of Physics, Arizona State University, Tempe, AZ, USA.
Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Department of Chemistry and Physics, ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Victoria, Australia.
X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA.
Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA.
Kenwood Interdisciplinary Research Complex Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany.
Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.73 kDa 
• Atom Count: 3,031 
• Modeled Residue Count: 142 
• Deposited Residue Count: 142 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
adenine riboswitch aptamer variant	A, B	71	Vibrio vulnificus

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE (Subject of Investigation/LOI)	C [auth A], F [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	E [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.279 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.09	α = 90.01
b = 25.49	β = 84.05
c = 123.96	γ = 68.89

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
CrystFEL	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-11 
Deposition Author(s): Stagno, J.R., Wang, Y.-X.

Revision History  

• Version 1.0: 2020-11-11
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 1.2: 2021-10-06
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Refinement description