9SYF
Beyond single-state RNA structural biology: MD/NMR description of temperature-sensitive dynamic RNA ensembles - GCAA MD conformational ensemble
Summary for 9SYF
| Entry DOI | 10.2210/pdb9syf/pdb |
| Related | 9SYD 9SYE |
| NMR Information | BMRB: 35023 |
| Descriptor | RNA hairpin with GCAA tetraloop (1 entity in total) |
| Functional Keywords | model hairpin, conformational ensemble, md, rna, gcaa, tetraloop, high resolution |
| Biological source | synthetic RNA |
| Total number of polymer chains | 1 |
| Total formula weight | 4500.76 |
| Authors | Leopold, D.,Oxenfarth, A.,Thomasen, F.E.,Kuemmerer, F.,Schnieders, R.,Pinter, G.,Wacker, A.,Jonker, H.R.A.,Fuertig, B.,Richter, C.,Lindorff-Larsen, K.,Schwalbe, H. (deposition date: 2025-10-11, release date: 2026-06-24, Last modification date: 2026-07-29) |
| Primary citation | Leopold, D.,Oxenfarth, A.,Thomasen, F.E.,Kummerer, F.,Schnieders, R.,Pinter, G.,Wacker, A.,Jonker, H.R.A.,Furtig, B.,Richter, C.,Lindorff-Larsen, K.,Schwalbe, H. Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops. Rna, 32:1199-1212, 2026 Cited by PubMed Abstract: While the GNRA tetraloops are an extensively studied and common RNA motif, their dynamic NMR structures in solution integrating state-of-the-art NMR parameters such as residual dipolar couplings (RDC) and cross correlated relaxation rates (CCR) have previously not been determined. Given their dominant occurrence among tetraloops in the PDB and the advance of experimentally reweighted MD simulations, the present work aims at investigating the entire conformational space of two known GNRA tetraloops sequences by an extensive NMR investigation of NOEs, J-couplings constants, RDCs and CCRs. As classical structure calculation proved insufficient for the more dynamic tetraloop we turned to Bayesian/maximum entropy reweighting of molecular simulations using our rich set of experiments. The resulting ensembles were clustered and compared to classically restrained structure calculations, structures from the PDB and models predicted by the prediction algorithms FarFar and Alphafold 3. Our results show that GNRA tetraloops can vary in dynamic sampling of conformational space. They highlight the importance of individual experimental validation of computationally obtained dynamic ensembles and model predictions. PubMed: 42215280DOI: 10.1261/rna.081067.126 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
Download full validation report
