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Structure. 2014 Oct 7;22(10):1528-37. doi: 10.1016/j.str.2014.08.007. Epub 2014 Sep 18.

Autofocused 3D classification of cryoelectron subtomograms.

Author information

1
Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Computer Aided Medical Procedures (CAMP), Technische Universität München, Boltzmannstrasse 3, 85748 Garching, Germany.
2
Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
3
National Centre for Biotechnology, National Research Council (CNB-CSIC), Campus UAM, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
4
Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address: foerster@biochem.mpg.de.

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.

PMID:
25242455
DOI:
10.1016/j.str.2014.08.007
[Indexed for MEDLINE]
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