EMatch: An efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

Oranit Dror*, Keren Lasker, Ruth Nussinov, Haim Wolfson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6-10 Å resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 Å resolution.

Original languageEnglish
Pages (from-to)42-49
Number of pages8
JournalActa Crystallographica Section D: Biological Crystallography
Volume63
Issue number1
DOIs
StatePublished - 13 Dec 2006

Keywords

  • Intermediate-resolution cryo-EM maps
  • Macromolecular assemblies
  • Structural bioinformatics
  • Three-dimensional alignment of secondary structures

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