6VWT

Transitional unit cell 1 of adenine riboswitch aptamer crystal phase transition upon ligand binding

Summary for 6VWT

• Entry DOI: 10.2210/pdb6vwt/pdb
• Related: 5E54
• Descriptor: adenine riboswitch aptamer variant, ADENINE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: riboswitch, phase transition, time-resolved, rna
• Biological source: Vibrio vulnificus
• Total number of polymer chains: 2
• Total formula weight: 45839.46

Authors

Stagno, J.R.,Wang, Y.-X. (deposition date: 2020-02-20, release date: 2020-11-11, Last modification date: 2023-10-11)

Primary citation

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.
Synchronous RNA conformational changes trigger ordered phase transitions in crystals.
Nat Commun, 12:1762-1762, 2021

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.

PubMed: 33741910
DOI: 10.1038/s41467-021-21838-5

Experimental method

X-RAY DIFFRACTION (3.03 Å)