title: Accurate model annotation of a near-atomic resolution cryo-EM map.
abstract: Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030.
authors.forename: Corey F
authors.initials: CF
authors.lastname: Hryc
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.
authors.forename: Dong-Hua
authors.initials: DH
authors.lastname: Chen
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
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, TX 77030.
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, TX 77030.
authors.forename: Zhao
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.
authors.forename: Cameron
authors.initials: C
authors.lastname: Haase-Pettingell
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.
authors.forename: Wen
authors.initials: W
authors.lastname: Jiang
authors.affiliation: Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: King
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030.|National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Schmid
authors.affiliation: Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030; wah@bcm.edu.|National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.
authors.forename: Wah
authors.initials: W
authors.lastname: Chiu
mesh_terms: D017100:Bacteriophage P22; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry; D020285:Cryoelectron Microscopy / Q000379:methods; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D015203:Reproducibility of Results
chemical_list: D036022:Capsid Proteins; D046911:Macromolecular Substances
keywords: P22; annotation; cryo-EM; model; structure