EMD-20755
Apo SAM-IV Riboswitch
EMD-20755
Single-particle3.7 Å
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Map released: 18/12/2019
Last modified: 20/03/2024
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
Sample: Apo SAM-IV Riboswitch
Fitted models: 6ues (Avg. Q-score: 0.359)
Deposition Authors: Zhang K
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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
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(2019) Nat Commun , 10 , 5511 - 5511
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.
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.