title: Improving the visualization of cryo-EM density reconstructions.
abstract: Cryo-electron microscopy yields 3D density maps of macromolecules from single-particle images, tomograms, or 2D crystals. An optimal visualization of the density map is important for its proper interpretation. We have developed a method to improve the visualization of density maps by using general statistical information about proteins for the sharpening process. In particular, the packing density of atoms is highly similar between different proteins, which allows for building a pseudo-atomic model to approximate the true mass distribution. From this model the radial structure factor and density value histogram are estimated and applied as constraints to the 3D reconstruction in reciprocal- and real-space, respectively. Interestingly, similar improvements are obtained when using the correct radial structure factor and density value histogram from a crystal structure. Thus, the estimated pseudo-atomic model yields a sufficiently accurate mass distribution to optimally sharpen a density map.
authors.affiliation: Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Spiegel
authors.affiliation: Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany.
authors.forename: A K
authors.initials: AK
authors.lastname: Duraisamy
authors.affiliation: Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich, 52428 Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany. Electronic address: gu.schroeder@fz-juelich.de.
authors.forename: G F
authors.initials: GF
authors.lastname: Schröder
mesh_terms: D018834:Chaperonin 60 / Q000737:chemistry*; D020285:Cryoelectron Microscopy / Q000379:methods*; D004926:Escherichia coli; D064429:Fatty Acid Synthases / Q000737:chemistry*; D008958:Models, Molecular; D009169:Mycobacterium tuberculosis / Q000201:enzymology; D017434:Protein Structure, Tertiary; D050916:TRPV Cation Channels / Q000737:chemistry*
chemical_list: D018834:Chaperonin 60; D050916:TRPV Cation Channels; C493922:Trpv1 protein, rat; D064429:Fatty Acid Synthases
keywords: B-factor sharpening; Cryo electron microscopy; Density histogram matching