6WLU

V. cholerae glycine riboswitch with glycine models, 5.7 Angstrom resolution

Summary for 6WLU

• Entry DOI: 10.2210/pdb6wlu/pdb
• Related: 6WLT
• EMDB information: 21831 21832 21833 21834 21835 21836 21838 21839 21840 21841 21842
• Descriptor: RNA (231-MER) (1 entity in total)
• Functional Keywords: aptamer, riboswitch, rna
• Biological source: Vibrio cholerae
• Total number of polymer chains: 1
• Total formula weight: 74753.42

Authors

Kappel, K.,Zhang, K.,Su, Z.,Watkins, A.M.,Kladwang, W.,Li, S.,Pintilie, G.,Topkar, V.V.,Rangan, R.,Zheludev, I.N.,Yesselman, J.D.,Chiu, W.,Das, R. (deposition date: 2020-04-20, release date: 2020-07-08, Last modification date: 2024-03-06)

Primary citation

Kappel, K.,Zhang, K.,Su, Z.,Watkins, A.M.,Kladwang, W.,Li, S.,Pintilie, G.,Topkar, V.V.,Rangan, R.,Zheludev, I.N.,Yesselman, J.D.,Chiu, W.,Das, R.
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures.
Nat.Methods, 17:699-707, 2020

PubMed Abstract: The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable subnanometer-resolution coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. This hybrid 'Ribosolve' pipeline detects and falsifies homologies and conformational rearrangements in 11 previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length Vibrio cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and the computer-designed ATP-TTR-3 aptamer with and without AMP. Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput.

PubMed: 32616928
DOI: 10.1038/s41592-020-0878-9

Experimental method

ELECTRON MICROSCOPY (5.7 Å)