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Autofocused 3D Classification of Cryoelectron Subtomograms

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons77858

Chen,  Yuxiang
Förster, Friedrich / Modeling of Protein Complexes, Max Planck Institute of Biochemistry, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons78500

Pfeffer,  Stefan
Förster, Friedrich / Modeling of Protein Complexes, Max Planck Institute of Biochemistry, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons77965

Förster,  Friedrich
Förster, Friedrich / Modeling of Protein Complexes, Max Planck Institute of Biochemistry, Max Planck Society;

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Citation

Chen, Y., Pfeffer, S., Jesus Fernandez, J., Sorzano, C. O. S., & Förster, F. (2014). Autofocused 3D Classification of Cryoelectron Subtomograms. STRUCTURE, 22(10), 1528-1537. doi:10.1016/j.str.2014.08.007.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0024-456F-9
Abstract
Classification of subtomograms obtained by cryoelectron tomography (cryo-ET) is a powerful approach to study the conformational landscapes of macromolecular complexes in situ. Major challenges in subtomogram classification are the low signal-to-noise ratio (SNR) of cryo-tomograms, their incomplete angular sampling, the unknown number of classes and the typically unbalanced abundances of structurally distinct complexes. Here, we propose a clustering algorithm named AC3D that is based on a similarity measure, which automatically focuses on the areas of major structural discrepancy between respective subtomogram class averages. Furthermore, we incorporate a spherical-harmonics-based fast subtomogram alignment algorithm, which provides a significant speedup. Assessment of our approach on simulated data sets indicates substantially increased classification accuracy of the presented method compared to two state-of-the-art approaches. Application to experimental subtomograms depicting endoplasmic-reticulum-associated ribosomal particles shows that AC3D is well suited to deconvolute the compositional heterogeneity of macromolecular complexes in situ.