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bioRxiv · 10.1101/2024.12.10.627647

Identification and cryoEM structure determination of Escherichia phage YDC107 tail found in a bacteria-contaminated buffer

Kopylov, M.·Bobe, D.·Jenkins, M. C.·Dutta, T.
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Abstract

Cryo-electron microscopy data analysis can yield multiple structures from a single heterogeneous dataset. Here, we show a workflow we used for the identification of a contaminant from a cryoEM grid without prior knowledge of protein sequence. We determined the tail structure of Escherichia phage YDC107 from only several thousand particles. The workflow combines high-resolution single-particle data processing with de novo model determination using ML-based methods. Structural analysis revealed that the central part of the phage tail has a C6 symmetry, however the overall symmetry of each segment is C3 due to dimerization of a flexible domain. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=67 SRC="FIGDIR/small/627647v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1444ae3org.highwire.dtl.DTLVardef@907ec1org.highwire.dtl.DTLVardef@71eebdorg.highwire.dtl.DTLVardef@1f0e6a1_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Kopylov, M., Bobe, D., Jenkins, M. C., Dutta, T.. 2024-12-11. Identification and cryoEM structure determination of Escherichia phage YDC107 tail found in a bacteria-contaminated buffer. https://doi.org/10.1101/2024.12.10.627647

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