PDBsum entry 6wlm

RNA

PDB id: 6wlm

Contents

DNA/RNA

PDB id:

6wlm

Name:

RNA

Title:

F. Nucleatum glycine riboswitch with glycine models, 7.4 angstrom resolution

Structure:

RNA (171-mer). Chain: a. Engineered: yes

Source:

Synthetic: yes. Fusobacterium nucleatum. Organism_taxid: 851

Ensemble:

20 models

Authors:

K.Kappel,K.Zhang,Z.Su,A.M.Watkins,W.Kladwang,S.Li,G.Pintilie, V.V.Topkar,R.Rangan,I.N.Zheludev,J.D.Yesselman,W.Chiu,R.Das

Key ref:

K.Kappel et al. (2020). Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nat Methods, 17, 699-707. PubMed id: 32616928 DOI: 10.1038/s41592-020-0878-9

Date:

20-Apr-20 Release date: 08-Jul-20

DNA/RNA chain

G-G-A-A-U-C-G-G-A-U-G-A-A-G-A-U-A-U-G-A-G-G-A-G-A-G-A-U-U-U-C-A-U-U-U-U-A-A-U- 171 bases

DOI no: 10.1038/s41592-020-0878-9

Nat Methods 17:699-707 (2020)

PubMed id: 32616928

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures.

K.Kappel, K.Zhang, Z.Su, A.M.Watkins, W.Kladwang, S.Li, G.Pintilie, V.V.Topkar, R.Rangan, I.N.Zheludev, J.D.Yesselman, W.Chiu, R.Das.

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.