Docking structures of domains into maps from cryo-electron microscopy using local correlation

Abstract

Accurate maps of large macromolecular complexes can be calculated from cryo-electron micrographs of non-crystalline specimens to resolutions of about 10 Å. A method to dock the atomic structures of domains solved by X-ray crystallography or nuclear magnetic resonance into cryo-EM maps is presented. Domains can be docked independently into large complexes without prior definition of the boundaries. No special symmetry is assumed and the procedure is suitable for general application to almost any system where a cryo-EM map (at 15 Å resolution or better) of a complex has been obtained and the atomic structures of the components are available. This is achieved through use of a real-space density-matching procedure based on local correlation. A complete asymmetric unit search correlating a density object derived from the atomic coordinates and the density of the EM map is performed. The correlation coefficient is calculated locally in real space using only values of the search object and corresponding samples extracted from the EM map which are under the 'footprint' of the positioned search object. The procedure has been demonstrated by docking the domains of GroEL from the crystal structure into a cryo-EM map Fourier filtered to 12 or 15 Å resolution. The correct positions were found without applying any additional constraints. A model of the oligomer built from the docked domains compared favourably with the known crystal structure, confirming the validity of the approach. The procedure is designed to facilitate the incorporation of additional constraints on the docking solutions, which could help to dock using lower resolution maps.