Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells

By D. Tegunov, Liang Xue, C. Dienemann, Patrick Cramer, J. Mahamid. Nature Methods, 2021

435 citations recorded by the source corpus.

Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and three-dimensional deformation during exposures are crucial for achieving high-resolution reconstructions. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement framework for cryo-EM data and couples a comprehensive spatial deformation model to in silico correction of electron-optical aberrations. M provides a unified optimization framework for both frame-series and tomographic tilt-series data. We show that tilt-series data can provide the same resolution as frame-series data on a purified protein specimen, indicating that the alignment step no longer limits the resolution obtainable from tomographic data. In combination with Warp and RELION, M resolves to residue level a 70S ribosome bound to an antibiotic inside intact bacterial cells. Our work provides a computational tool that facilitates structural biology in cells. The software M establishes a reference-based multi-particle refinement framework for cryo-EM data. Combined with CTF correction and map denoising, M enables residue-level structure determination inside cells.

Subfields: Radiation, Structural Biology, Surfaces, Coatings and Films

View Paper: https://www.semanticscholar.org/paper/2b96f406046a0e0392296afc9c8657565f1576a7

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In Structural Biology

1. Tristan Cragnolini
2. J. Beton
3. Maya Topf
4. Thomas Mulvaney
5. Manaz Kaleel
6. Aaron Sweeney

In Surfaces, Coatings and Films

1. J. Beton
2. Maya Topf
3. Tristan Cragnolini
4. Thomas Mulvaney
5. Manaz Kaleel
6. Aaron Sweeney

Citations in the corpus

• Plasmodium 6-Cysteine Proteins: Functional Diversity, Transmission-Blocking Antibodies and Structural Scaffolds (2022, background): “…P. falciparum proteins, namely Pf36, Pf52, PfLISP2, PfB9, Pf12, Pf12p, Pf41, Pf38, Pf92, Pfs48/45, Pfs230, Pfs230p, Pfs47 and PfPSOP12 (Figure 1A) (Templeton and Kaslow, 1999; Kappe et al., 2001; Thompson et al., 2001; Gardner et al., 2002; Gerloff et al., 2005; Arredondo et al., 2012; Orito et…”
• Integrating model simulation tools and cryo‐electron microscopy (2022, background): “5 Å.(2,8) Indeed, for a subset of sufficiently stable samples, true atomistic resolution is now achievable by cryo-EM.”