Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

Javier Velázquez-Muriel, Keren Lasker, Daniel Russel, Jeremy Phillips, Benjamin M. Webb, Dina Schneidman-Duhovny, Andrej Sali*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

37 Scopus citations


To obtain a structural model of a macromolecular assembly by single-particle EM, a large number of particle images need to be collected, aligned, clustered, averaged, and finally assembled via reconstruction into a 3D density map. This process is limited by the number and quality of the particle images, the accuracy of the initial model, and the compositional and conformational heterogeneity. Here, we describe a structure determination method that avoids the reconstruction procedure. The atomic structures of the individual complex components are assembled by optimizing a match against 2D EM class-average images, an excluded volume criterion, geometric complementarity, and optional restraints from proteomics and chemical cross-linking experiments. The optimization relies on a simulated annealing Monte Carlo search and a divide-and-conquer message-passing algorithm. Using simulated and experimentally determined EM class averages for 12 and 4 protein assemblies, respectively, we showthat a few class averages can indeed result in accurate models for complexes of as many as five subunits. Thus, integrative structural biology can now benefit from the relative ease with which the EM class averages are determined.

Original languageAmerican English
Pages (from-to)18821-18826
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number46
StatePublished - 13 Nov 2012
Externally publishedYes


  • Computational biology
  • Integrative modeling
  • Structural determination


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