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

Abstract

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.

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1];  [1]; ORCiD logo [1];  [2]; ORCiD logo [3]; ORCiD logo [1];  [3]
  1. Stanford Univ., CA (United States)
  2. Univ. of Montana, Missoula, MT (United States)
  3. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL); Stanford Univ., CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
National Science Foundation (NSF); National Institutes of Health (NIH); USDOE Office of Science (SC)
OSTI Identifier:
1594993
Grant/Contract Number:  
AC02-76SF00515; P41GM103832; R01GM079429; U54GM103297; P20GM103546; GM112579; R21AI145647
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Zhang, Kaiming, Li, Shanshan, Kappel, Kalli, Pintilie, Grigore, Su, Zhaoming, Mou, Tung-Chung, Schmid, Michael F., Das, Rhiju, and Chiu, Wah. Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. United States: N. p., 2019. Web. doi:10.1038/s41467-019-13494-7.
Zhang, Kaiming, Li, Shanshan, Kappel, Kalli, Pintilie, Grigore, Su, Zhaoming, Mou, Tung-Chung, Schmid, Michael F., Das, Rhiju, & Chiu, Wah. Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. United States. doi:10.1038/s41467-019-13494-7.
Zhang, Kaiming, Li, Shanshan, Kappel, Kalli, Pintilie, Grigore, Su, Zhaoming, Mou, Tung-Chung, Schmid, Michael F., Das, Rhiju, and Chiu, Wah. Tue . "Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution". United States. doi:10.1038/s41467-019-13494-7. https://www.osti.gov/servlets/purl/1594993.
@article{osti_1594993,
title = {Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution},
author = {Zhang, Kaiming and Li, Shanshan and Kappel, Kalli and Pintilie, Grigore and Su, Zhaoming and Mou, Tung-Chung and Schmid, Michael F. and Das, Rhiju and Chiu, Wah},
abstractNote = {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.},
doi = {10.1038/s41467-019-13494-7},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {12}
}

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