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TitleStreamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 6543, Year 2023
Publish dateOct 17, 2023
AuthorsNikita Balyschew / Artsemi Yushkevich / Vasilii Mikirtumov / Ricardo M Sanchez / Thiemo Sprink / Mikhail Kudryashev /
PubMed AbstractStructures of macromolecules in their native state provide unique unambiguous insights into their functions. Cryo-electron tomography combined with subtomogram averaging demonstrated the power to ...Structures of macromolecules in their native state provide unique unambiguous insights into their functions. Cryo-electron tomography combined with subtomogram averaging demonstrated the power to solve such structures in situ at resolutions in the range of 3 Angstrom for some macromolecules. In order to be applicable to the structural determination of the majority of macromolecules observable in cells in limited amounts, processing of tomographic data has to be performed in a high-throughput manner. Here we present TomoBEAR-a modular configurable workflow engine for streamlined processing of cryo-electron tomographic data for subtomogram averaging. TomoBEAR combines commonly used cryo-EM packages with reasonable presets to provide a transparent ("white box") approach for data management and processing. We demonstrate applications of TomoBEAR to two data sets of purified macromolecular targets, to an ion channel RyR1 in a membrane, and the tomograms of plasma FIB-milled lamellae and demonstrate the ability to produce high-resolution structures. TomoBEAR speeds up data processing, minimizes human interventions, and will help accelerate the adoption of in situ structural biology by cryo-ET. The source code and the documentation are freely available.
External linksNat Commun / PubMed:37848413 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution2.8 - 8.9 Å
Structure data

EMDB-17232: Purified human apoferritin at 2.8 A resolution from tilt series processed with TomoBEAR
Method: EM (subtomogram averaging) / Resolution: 2.8 Å

EMDB-17272: Structure of RyR1 obtained from SR vesicles tilt series (EMPIAR-10452), reprocessed with TomoBEAR
Method: EM (subtomogram averaging) / Resolution: 8.9 Å

EMDB-18505: Human 80S ribosome structure from pFIB-lamellae reprocessed with TomoBEAR
Method: EM (subtomogram averaging) / Resolution: 6.2 Å

Source
  • Homo sapiens (human)
  • Oryctolagus cuniculus (rabbit)

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