title: Autofocused 3D classification of cryoelectron subtomograms.
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.
authors.affiliation: 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.
authors.forename: Yuxiang
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Pfeffer
authors.affiliation: National Centre for Biotechnology, National Research Council (CNB-CSIC), Campus UAM, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
authors.forename: José Jesús
authors.initials: JJ
authors.lastname: Fernández
authors.affiliation: National Centre for Biotechnology, National Research Council (CNB-CSIC), Campus UAM, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
authors.forename: Carlos Oscar S
authors.initials: CO
authors.lastname: Sorzano
authors.affiliation: Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address: foerster@biochem.mpg.de.
authors.forename: Friedrich
authors.initials: F
authors.lastname: Förster
mesh_terms: D000465:Algorithms; D020285:Cryoelectron Microscopy / Q000379:methods*; D055032:Electron Microscope Tomography / Q000379:methods*; D004721:Endoplasmic Reticulum / Q000378:metabolism; D021621:Imaging, Three-Dimensional / Q000379:methods*; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D012270:Ribosomes / Q000737:chemistry / Q000378:metabolism; D059629:Signal-To-Noise Ratio; D057188:Workflow
chemical_list: D046911:Macromolecular Substances