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TitleA Bayesian approach to single-particle electron cryo-tomography in RELION-4.0.
Journal, issue, pagesElife, Vol. 11, Year 2022
Publish dateDec 5, 2022
AuthorsJasenko Zivanov / Joaquín Otón / Zunlong Ke / Andriko von Kügelgen / Euan Pyle / Kun Qu / Dustin Morado / Daniel Castaño-Díez / Giulia Zanetti / Tanmay A M Bharat / John A G Briggs / Sjors H W Scheres /
PubMed AbstractWe present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are ...We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe the approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt-series alignments, beam-induced motions of the particles throughout the tilt-series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, particularly for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.
External linksElife / PubMed:36468689 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution3.0 - 3.8 Å
Structure data

15949

8bsh

EMDB-15949: COPII inner coat reprocessed with relion4.0
PDB-8bsh: COPII inner coat
Method: EM (subtomogram averaging) / Resolution: 3.8 Å

16183

8bqe

EMDB-16183, PDB-8bqe:
In situ structure of the Caulobacter crescentus S-layer
Method: EM (subtomogram averaging) / Resolution: 3.5 Å

EMDB-16207: HIV-1 CA-SP1 subtomogram average with Relion4 from EMPIAR-10164 dataset, 3.2 A from 5 tomograms
Method: EM (subtomogram averaging) / Resolution: 3.2 Å

EMDB-16209: HIV-1 CA-SP1 subtomogram average with Relion4 from EMPIAR-10164 dataset, 3.0 A from the full dataset
Method: EM (subtomogram averaging) / Resolution: 3.0 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • Saccharomyces cerevisiaeaSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
  • caulobacter vibrioides na1000 (bacteria)
KeywordsSTRUCTURAL PROTEIN / RsaA S-layer sub-tomogram averaging Caulobacter / PROTEIN TRANSPORT / COPII

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