Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution

• Published in: Nature communications Vol. 10; no. 1; pp. 5511 - 6
• Main Authors: Zhang, Kaiming, Li, Shanshan, Kappel, Kalli, Pintilie, Grigore, Su, Zhaoming, Mou, Tung-Chung, Schmid, Michael F., Das, Rhiju, Chiu, Wah
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03.12.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 631/45/500; 631/535/1258/1259; Adenosylmethionine; Antibiotics; BASIC BIOLOGICAL SCIENCES; Binding; Cryoelectron Microscopy; Drug development; Electron microscopy; Homology; Humanities and Social Sciences; Ligands; Metabolism; Molecular Weight; multidisciplinary; Nucleic Acid Conformation; Ribonucleic acid; Riboswitch; Riboswitches; RNA; S-Adenosylmethionine; S-Adenosylmethionine - chemistry; Science; Science (multidisciplinary); Sulfur
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-13494-7

Specimens below 50 kDa have generally been considered too small to be analyzed by single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it difficult to obtain high-resolution structures by cryo-EM. In bacteria, riboswitches regulate sulfur metabolism through binding to the S-adenosylmethionine (SAM) ligand and offer compelling targets for new antibiotics. SAM-I, SAM-I/IV, and SAM-IV are the three most commonly found SAM riboswitches, but the structure of SAM-IV is still unknown. Here, we report the structures of apo and SAM-bound SAM-IV riboswitches (119-nt, ~40 kDa) to 3.7 Å and 4.1 Å resolution, respectively, using cryo-EM. The structures illustrate homologies in the ligand-binding core but distinct peripheral tertiary contacts in SAM-IV compared to SAM-I and SAM-I/IV. Our results demonstrate the feasibility of resolving small RNAs with enough detail to enable detection of their ligand-binding pockets and suggest that cryo-EM could play a role in structure-assisted drug design for RNA. The conformational heterogeneity of RNA molecules makes their structure determination by X-ray crystallography and NMR challenging. Here the authors show that RNA structures can be solved by cryo-EM and present the structures of a 40 kDa SAM-IV riboswitch in the apo form and bound to its ligand S-adenosylmethionine.