Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1

By Jasenko Zivanov, Takanori Nakane, Sjors H. W. Scheres. 2019

632 citations recorded by the source corpus.

We present methods that detect three types of aberrations in single-particle cryo-EM data sets: symmetrical and antisymmetrical optical aberrations and magnification anisotropy. Because our methods only depend on the availability of a preliminary 3D reconstruction from the data, they can be used to correct for these aberrations for any given cryo-EM data set, a posteriori. Using five publicly available data sets, we show that considering these aberrations improves the resolution of the 3D reconstruction when the effects are present. The methods are implemented in version 3.1 of our open-source software package RELION.

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

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Structural Biology

1. H. Kratzat
2. Nieng Yan
3. Roland Beckmann
4. O. Berninghausen
5. R. Buschauer

In Surfaces, Coatings and Films

1. H. Kratzat
2. Nieng Yan
3. Roland Beckmann
4. O. Berninghausen
5. R. Buschauer

Citations in the corpus

• Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH (2022, methodology): “Third, the top AlphaFold2 model and P 2 1 2 1 2 1 / C 2-structure derived homology models (r.m.s.d. 0.7/0.8 Å) of D10C were individually rigidly docked with UCSF Chimera into the 3D reconstruction of full-length UMOD (overall nominal resolution 4.7 Å) 6 , whose masking and postprocessing with RELION”
• Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade (2022, neutral): “After one round of CTF refinement ( Zivanov et al., 2020 ), the particles were subjected to another round of Bayesian polishing, and the resulting shiny particles were imported back into cryoSPARC.”
• Cryo-EM analysis of a membrane protein embedded in the liposome (2020, background): “1-beta’s own interpretation with a 5 × 5 patch and a twofold binning (46).”
• Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2 (2020, methodology): “Materials and methods Figures S1-S5 Tables S1-S2 References (47-61)”
• Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice (2021, neutral): “Merged particles weresubjected to multiple rounds of CTF Refinement (beam tilt, trefoil, fourth order aberrations, anisotropic magnification, and per-particle defocus and astigmatism) and Bayesian Polishing (70), followed by another round of 2D classification.”