De novo computational RNA modeling into cryoEM maps of large ribonucleoprotein complexes
By K. Kappel, Shiheng Liu, K. Larsen, G. Skiniotis, E. V. Puglisi, Joseph D. Puglisi, Z. H. Zhou, R. Zhao, Rhiju Das. 2018
65 citations recorded by the source corpus.
Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA–protein assemblies, but nearly all maps determined with this method have biologically important regions where the local resolution does not permit RNA coordinate tracing. To address these omissions, we present de novo ribonucleoprotein modeling in real space through assembly of fragments together with experimental density in Rosetta (DRRAFTER). We show that DRRAFTER recovers near-native models for a diverse benchmark set of RNA–protein complexes including the spliceosome, mitochondrial ribosome, and CRISPR–Cas9–sgRNA complexes; rigorous blind tests include yeast U1 snRNP and spliceosomal P complex maps. Additionally, to aid in model interpretation, we present a method for reliable in situ estimation of DRRAFTER model accuracy. Finally, we apply DRRAFTER to recently determined maps of telomerase, the HIV-1 reverse transcriptase initiation complex, and the packaged MS2 genome, demonstrating the acceleration of accurate model building in challenging cases. DRRAFTER, a method for RNA modeling into cryo-EM maps, generates accurate models for diverse RNA–protein complexes.
Subfields: Molecular Biology
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In Molecular Biology
- Andrew M. Watkins
- R. Rangan
- Rhiju Das
- Jeffrey J. Gray
- David Baker
- Frank DiMaio
- Brian D. Weitzner
- Fang-Chieh Chou
Citations in the corpus
- FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds (2020, unknown): “Recently, extensions of FARFAR to building coordinates into RNA-protein (Kappel et al., 2018) and RNA-only electron density maps (Kappel et al., 2019) have suggested a promising approach.”
- RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli–Pepper aptamer FRET pair (2023, unknown): “Since we obtained the cryo-EM map before the publication of the Pepper crystal structures (35), we attempted structure determination using the DRRAFTER pipeline (51,52).”
- Using Rosetta for RNA homology modeling (2019, background): “As expected from this convergence level (Kappel et al., 2018), the models were also accurate compared to the actual experimental structure of”