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TitleMiLoPYP: self-supervised molecular pattern mining and particle localization in situ.
Journal, issue, pagesNat Methods, Year 2024
Publish dateSep 9, 2024
AuthorsQinwen Huang / Ye Zhou / Alberto Bartesaghi /
PubMed AbstractCryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to ...Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to obtain near-atomic resolution structures of frequently occurring macromolecules within their native environment. Two outstanding challenges associated with cryo-electron tomography/single-particle tomography are the automatic identification and localization of proteins, tasks that are hindered by the molecular crowding inside cells, imaging distortions characteristic of cryo-electron tomography tomograms and the sheer size of tomographic datasets. Current methods suffer from low accuracy, demand extensive and time-consuming manual labeling or are limited to the detection of specific types of proteins. Here, we present MiLoPYP, a two-step dataset-specific contrastive learning-based framework that enables fast molecular pattern mining followed by accurate protein localization. MiLoPYP's ability to effectively detect and localize a wide range of targets including globular and tubular complexes as well as large membrane proteins, will contribute to streamline and broaden the applicability of high-resolution workflows for in situ structure determination.
External linksNat Methods / PubMed:39251798
MethodsEM (subtomogram averaging)
Resolution5.0 - 37.0 Å
Structure data

EMDB-45261: CryoEM reconstruction of 70S ribosome from EMPIAR-10304
Method: EM (subtomogram averaging) / Resolution: 5.0 Å

EMDB-45266: Structure of 70S ribosome from EMPIAR-10499
Method: EM (subtomogram averaging) / Resolution: 5.4 Å

EMDB-45267: Open state SARS-COV2 spike protein from EMPIAR-10453
Method: EM (subtomogram averaging) / Resolution: 5.6 Å

EMDB-45268: Structure of closed state SARS-Cov2 spike protein from EMPIAR-10453
Method: EM (subtomogram averaging) / Resolution: 9.3 Å

EMDB-45269: Structure of RuBisCO from EMPIAR-10694
Method: EM (subtomogram averaging) / Resolution: 13.0 Å

EMDB-45270: Structure of 80S ribosome from EMPIAR-10987
Method: EM (subtomogram averaging) / Resolution: 8.6 Å

EMDB-45271: Structure of microtubule from EMPIAR-10987
Method: EM (subtomogram averaging) / Resolution: 37.0 Å

EMDB-45272: Structure of ATP synthase from EMPIAR-11658
Method: EM (subtomogram averaging) / Resolution: 13.0 Å

Source
  • Escherichia coli DH5[alpha] (bacteria)
  • Mycoplasmoides pneumoniae 19294 (bacteria)
  • Chlamydomonas reinhardtii (plant)
  • Mus musculus (house mouse)
  • Saccharomyces cerevisiae (brewer's yeast)

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