6UET

SAM-bound SAM-IV riboswitch

Summary for 6UET

• Entry DOI: 10.2210/pdb6uet/pdb
• EMDB information: 20755 20756
• Descriptor: RNA (119-MER), S-ADENOSYLMETHIONINE (2 entities in total)
• Functional Keywords: sam-iv riboswitch, cryo-em, small rna, rna
• Biological source: Mycobacterium sp. MCS
• Total number of polymer chains: 1
• Total formula weight: 38921.34

Authors

Zhang, K.,Li, S.,Kappel, K.,Pintilie, G.,Su, Z.,Mou, T.,Schmid, M.,Das, R.,Chiu, W. (deposition date: 2019-09-23, release date: 2019-12-18, Last modification date: 2024-03-20)

Primary citation

Zhang, K.,Li, S.,Kappel, K.,Pintilie, G.,Su, Z.,Mou, T.C.,Schmid, M.F.,Das, R.,Chiu, W.
Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 angstrom resolution.
Nat Commun, 10:5511-5511, 2019

PubMed 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.

PubMed: 31796736
DOI: 10.1038/s41467-019-13494-7

Experimental method

ELECTRON MICROSCOPY (4.1 Å)