9FM4

Dynamic structure of the apical stem loop of the stem loop 2 motif (s2m) from SCoV-2 Delta variant

Summary for 9FM4

• Entry DOI: 10.2210/pdb9fm4/pdb
• NMR Information: BMRB: 34919
• Descriptor: RNA (25-MER) (1 entity in total)
• Functional Keywords: s2m, covid-19, nmr assignment, molecular dynamic simulations, nmr dynamics, rna
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 1
• Total formula weight: 8068.86

Authors

Wirtz Martin, M.A.,Matzel, T.,Makowski, J.,Kensinger, A.,Herr, A.,Wacker, A.,Richter, C.,Jonker, H.R.A.,Evanseck, J.,Schwalbe, H. (deposition date: 2024-06-05, release date: 2025-05-07, Last modification date: 2025-07-16)

Primary citation

Wirtz Martin, M.A.,Makowski, J.A.,Matzel, T.,Kensinger, A.H.,Herr, A.,Richter, C.,Jonker, H.R.A.,Wacker, A.,Evanseck, J.D.,Schwalbe, H.
Structural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: In structured RNAs, helical elements are often capped by apical loops that are integral structural elements, ranging from 3 to >20 nts of size on average, and display a highly heterogeneous energy landscape profile, rendering structural characterization particularly challenging. We here provide a characterization of the SARS-CoV-2 Delta s2m element containing a highly dynamic nonaloop using an integrative approach of nuclear magnetic resonance spectroscopy (NMR), small angle X-ray scattering (SAXS), and molecular dynamics simulations (MD). We further explored the conformational space in the s2m nonaloop and its transient closing 5'-G-U-3' base pair by MD simulations weighted by experimental NMR observables, leading to a comprehensive representation of the s2m nonaloop motif. Our deconvolution of the ensemble into conformations and dynamics provides a basis for future ensemble-functional characterization of RNA structures featuring dynamic motifs.

PubMed: 40586311
DOI: 10.1093/nar/gkaf552

Experimental method

SOLUTION NMR
SOLUTION SCATTERING