4TZY

Vibrio vulnificus Adenine Riboswitch Variant, grown in both Sr2+ and Mg2+

Summary for 4TZY

• Entry DOI: 10.2210/pdb4tzy/pdb
• Related: 4TZP 4TZV 4TZW 4TZX 4TZZ
• Descriptor: Vibrio vulnificus Adenine Riboswitch, ADENINE, STRONTIUM ION, ... (5 entities in total)
• Functional Keywords: rna, riboswitch, gene regulation, adenine
• Biological source: Vibrio vulnificus
• Total number of polymer chains: 1
• Total formula weight: 23484.46

Authors

Zhang, J.,Ferre-D'Amare, A.R. (deposition date: 2014-07-11, release date: 2014-09-10, Last modification date: 2023-09-27)

Primary citation

Zhang, J.,Ferre-D'Amare, A.R.
Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.
Structure, 22:1363-1371, 2014

PubMed Abstract: Compared to globular proteins, RNAs with complex 3D folds are characterized by poorly differentiated molecular surfaces dominated by backbone phosphates, sparse tertiary contacts stabilizing global architecture, and conformational flexibility. The resulting generally poor order of crystals of large RNAs and their complexes frequently hampers crystallographic structure determination. We describe and rationalize a postcrystallization treatment strategy that exploits the importance of solvation and counterions for RNA folding. Replacement of Li(+) and Mg(2+) needed for growth of crystals of a tRNA-riboswitch-protein complex with Sr(2+), coupled with dehydration, dramatically improved the resolution limit (8.5-3.2 Å) and data quality, enabling structure determination. The soft Sr(2+) ion forms numerous stabilizing intermolecular contacts. Comparison of pre- and posttreatment structures reveals how RNA assemblies redistribute as quasi-rigid bodies to yield improved crystal packing. Cation exchange complements previously reported postcrystallization dehydration of protein crystals and represents a potentially general strategy for improving crystals of large RNAs.

PubMed: 25185828
DOI: 10.1016/j.str.2014.07.011

Experimental method

X-RAY DIFFRACTION (2.57 Å)