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TitleLearning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN.
Journal, issue, pagesbioRxiv, Year 2023
Publish dateJun 2, 2023
AuthorsBarrett M Powell / Joseph H Davis /
PubMed AbstractCryo-electron tomography (cryo-ET) allows one to observe macromolecular complexes in their native, spatially contextualized environment. Tools to visualize such complexes at nanometer resolution via ...Cryo-electron tomography (cryo-ET) allows one to observe macromolecular complexes in their native, spatially contextualized environment. Tools to visualize such complexes at nanometer resolution via iterative alignment and averaging are well-developed but rely on assumptions of structural homogeneity among the complexes under consideration. Recently developed downstream analysis tools allow for some assessment of macromolecular diversity but have limited capacity to represent highly heterogeneous macromolecules, including those undergoing continuous conformational changes. Here, we extend the highly expressive cryoDRGN deep learning architecture, originally created for cryo-electron microscopy single particle analysis, to sub-tomograms. Our new tool, tomoDRGN, learns a continuous low-dimensional representation of structural heterogeneity in cryo-ET datasets while also learning to reconstruct a large, heterogeneous ensemble of structures supported by the underlying data. Using simulated and experimental data, we describe and benchmark architectural choices within tomoDRGN that are uniquely necessitated and enabled by cryo-ET data. We additionally illustrate tomoDRGN's efficacy in analyzing an exemplar dataset, using it to reveal extensive structural heterogeneity among ribosomes imaged .
External linksbioRxiv / PubMed:37398315 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution3.5 - 26.0 Å
Structure data

EMDB-43285: Human heavy-chain holoferritin refined in C1 from cryo-ET data filtered by tomoDRGN
Method: EM (subtomogram averaging) / Resolution: 10.5 Å

EMDB-43286: Human heavy-chain apoferritin refined in C1 from cryo-ET data filtered by tomoDRGN
Method: EM (subtomogram averaging) / Resolution: 3.5 Å

EMDB-43287: Membrane-associated 70S ribosome in complex with SecDF
Method: EM (subtomogram averaging) / Resolution: 26.0 Å

Source
  • Homo sapiens (human)
  • Mycoplasmoides pneumoniae M129 (bacteria)

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