EMD-20755

Single-particle
3.7 Å
EMD-20755 Deposition: 23/09/2019
Map released: 18/12/2019
Last modified: 20/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-20755

Apo SAM-IV Riboswitch

EMD-20755

Single-particle
3.7 Å
EMD-20755 Deposition: 23/09/2019
Map released: 18/12/2019
Last modified: 20/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Helicobacter pylori, Mycobacterium sp. MCS
Sample: Apo SAM-IV Riboswitch
Fitted models: 6ues (Avg. Q-score: 0.359)

Deposition Authors: Zhang K , Li S
Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 angstrom resolution.
Zhang K , Li S , Kappel K , Pintilie G , Su Z , Mou TC, Schmid MF , Das R , Chiu W
(2019) Nat Commun , 10 , 5511 - 5511
PUBMED: 31796736
DOI: doi:10.1038/s41467-019-13494-7
ISSN: 2041-1723
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.