Using a partial atomic model from medium- resolution cryo-EM to solve a large crystal structure

Open Access

Abstract

Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallo­graphic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-modification procedures using rotation matrices and a mask based on the cryo-EM structure were critical for solving the structure. A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-EM map for molecular replacement. ; The following funding is acknowledged: Ministry of Science, Innovation and Universities of Spain (grant Nos. BFU2014-53550-P and BFU2017-83720-P to Miquel Coll; grant No. BFU2014-54181 to Jose´ L. Carrascosa; contract No. SEV2013-0347 to Ana Cuervo; contract No. RYC-2011-09071 to Cristina Machon; award No. SEV-2015-0500 to IRB Barcelona; award No. MDM-2014-0435 to IBMB Structural Biology Unit); Catalan Government CERCA Programme (grant to IRB Barcelona).