title: An atomic model of brome mosaic virus using direct electron detection and real-space optimization.
abstract: Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.
authors.affiliation: 1] National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2].
authors.forename: Zhao
authors.initials: Z
authors.lastname: Wang
authors.affiliation: 1] National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA [3].
authors.forename: Corey F
authors.initials: CF
authors.lastname: Hryc
authors.affiliation: Direct Electron LP, San Diego, California 92128, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Bammes
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Afonine
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Joanita
authors.initials: J
authors.lastname: Jakana
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Dong-Hua
authors.initials: DH
authors.lastname: Chen
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Xiangan
authors.initials: X
authors.lastname: Liu
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Baker
authors.affiliation: Department of Molecular &Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA.
authors.forename: Cheng
authors.initials: C
authors.lastname: Kao
authors.affiliation: 1] National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Ludtke
authors.affiliation: 1] National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Schmid
authors.affiliation: 1] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] Department of Bioengineering, University of California, Berkeley, California 94720, USA.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.affiliation: 1] National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Wah
authors.initials: W
authors.lastname: Chiu
mesh_terms: D017795:Bromovirus / Q000648:ultrastructure*; D020285:Cryoelectron Microscopy / Q000295:instrumentation / Q000379:methods*; D018360:Crystallography, X-Ray; D004583:Electrons; D007091:Image Processing, Computer-Assisted / Q000706:statistics & numerical data*; D008958:Models, Molecular; D011487:Protein Conformation