title: SPRING - an image processing package for single-particle based helical reconstruction from electron cryomicrographs.
abstract: Helical reconstruction from electron cryomicrographs has become a routine technique for macromolecular structure determination of helical assemblies since the first days of Fourier-based three-dimensional image reconstruction. In the past decade, the single-particle technique has had an important impact on the advancement of helical reconstruction. Here, we present the software package SPRING that combines Fourier based symmetry analysis and real-space helical processing into a single workflow. One of the most time-consuming steps in helical reconstruction is the determination of the initial symmetry parameters. First, we propose a class-based helical reconstruction approach that enables the simultaneous exploration and evaluation of many symmetry combinations at low resolution. Second, multiple symmetry solutions can be further assessed and refined by single-particle based helical reconstruction using the correlation of simulated and experimental power spectra. Finally, the 3D structure can be determined to high resolution. In order to validate the procedure, we use the reference specimen Tobacco Mosaic Virus (TMV). After refinement of the helical symmetry, a total of 50,000 asymmetric units from two micrographs are sufficient to reconstruct a subnanometer 3D structure of TMV at 6.4Å resolution. Furthermore, we introduce the individual programs of the software and discuss enhancements of the helical reconstruction workflow. Thanks to its user-friendly interface and documentation, SPRING can be utilized by the novice as well as the expert user. In addition to the study of well-ordered helical structures, the development of a streamlined workflow for single-particle based helical reconstruction opens new possibilities to analyze specimens that are heterogeneous in symmetries.
authors.affiliation: EMBL - European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69917 Heidelberg, Germany; Univ. Grenoble Alpes, UVHCI, F-38000 Grenoble, France; CNRS, UVHCI, F-38000 Grenoble, France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France.
authors.forename: Ambroise
authors.initials: A
authors.lastname: Desfosses
authors.affiliation: EMBL - European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69917 Heidelberg, Germany.
authors.forename: Rodolfo
authors.initials: R
authors.lastname: Ciuffa
authors.affiliation: Univ. Grenoble Alpes, UVHCI, F-38000 Grenoble, France; CNRS, UVHCI, F-38000 Grenoble, France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France.
authors.forename: Irina
authors.initials: I
authors.lastname: Gutsche
authors.affiliation: EMBL - European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69917 Heidelberg, Germany. Electronic address: carsten.sachse@embl.de.
authors.forename: Carsten
authors.initials: C
authors.lastname: Sachse
mesh_terms: D020285:Cryoelectron Microscopy / Q000379:methods*; D004583:Electrons; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D017433:Protein Structure, Secondary; D012984:Software; D014027:Tobacco Mosaic Virus / Q000737:chemistry
keywords: 3D reconstruction; Electron cryomicroscopy; Helical assembly; Helical symmetry; Image processing; Software