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Structure. 2008 Feb;16(2):295-307. doi: 10.1016/j.str.2007.11.016.

Protein structure fitting and refinement guided by cryo-EM density.

Author information

1
School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom. m.topf@cryst.bbk.ac.uk

Abstract

For many macromolecular assemblies, both a cryo-electron microscopy map and atomic structures of its component proteins are available. Here we describe a method for fitting and refining a component structure within its map at intermediate resolution (<15 A). The atomic positions are optimized with respect to a scoring function that includes the crosscorrelation coefficient between the structure and the map as well as stereochemical and nonbonded interaction terms. A heuristic optimization that relies on a Monte Carlo search, a conjugate-gradients minimization, and simulated annealing molecular dynamics is applied to a series of subdivisions of the structure into progressively smaller rigid bodies. The method was tested on 15 proteins of known structure with 13 simulated maps and 3 experimentally determined maps. At approximately 10 A resolution, Calpha rmsd between the initial and final structures was reduced on average by approximately 53%. The method is automated and can refine both experimental and predicted atomic structures.

PMID:
18275820
PMCID:
PMC2409374
DOI:
10.1016/j.str.2007.11.016
[Indexed for MEDLINE]
Free PMC Article
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