Symmetry-restrained flexible fitting for symmetric em maps

Kwok Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor Sewell, Klaus Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

Many large biological macromolecules have inherent structural symmetry, being composed of a few distinct subunits, repeated in a symmetric array. These complexes are often not amenable to traditional high-resolution structural determination methods, but can be imaged in functionally relevant states using cryo-electron microscopy (cryo-EM). A number of methods for fitting atomic-scale structures into cryo-EM maps have been developed, including the molecular dynamics flexible fitting (MDFF) method. However, quality and resolution of the cryo-EM map are the major determinants of a method's success. In order to incorporate knowledge of structural symmetry into the fitting procedure, we developed the symmetry-restrained MDFF method. The new method adds to the cryo-EM map-derived potential further restraints on the allowed conformations of a complex during fitting, thereby improving the quality of the resultant structure. The benefit of using symmetry-based restraints during fitting, particularly for medium to low-resolution data, is demonstrated for three different systems.

Original languageEnglish (US)
Pages (from-to)1211-1218
Number of pages8
JournalStructure
Volume19
Issue number9
DOIs
StatePublished - Sep 7 2011

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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