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Hryc, CF, Chen, DH, Afonine, PV, Jakana, J, Wang, Z, Haase-Pettingell, C, Jiang, W, Adams, PD, King, JA, Schmid, MF and Chiu, W (2017) Accurate model annotation of a near-atomic resolution cryo-EM map. Proc. Natl. Acad. Sci. U.S.A. 114:3103-3108
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.
|Gene product||Qualifier||GO Term||Evidence Code||with/from||Aspect||Extension||Notes||Status|
|GO:0039620: T=7 icosahedral viral capsid||
Gp5 of Salmonella phage P22 was shown to fold into a classical HK97 capsid fold (PMID:11000116). Figure 1b shows a density map of the P22 capsid cryo-EM model. From the cryo-EM image, one asymmetrical unit, outlined in red in Figure 1b, was modeled and presented in Figure 1c with seven different colors representing each of the seven proteins folding into a T=7 icosahedral structure. This cryo-EM derived model of the protein matched closely to the molecular model of the gp5 430 amino acid sequence shown in Figure 2b. This 430 amino acid sequence number corresponds to the BLAST sequence in Uniprot for gp5, confirming that the model derived from the cryo-EM imaging was indeed gp5.
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