Abstract
The resolution of electron-potential maps in single-particle cryo-electron microscopy (cryoEM) is approaching atomic or near- atomic resolution. However, no program currently exists for de novo cryoEM model building at resolutions exceeding beyond 3.5 Å. Here, we present a program, EMBuilder, based on template matching, to generate cryoEM models at high resolution. The program identifies features in both secondary-structure and Cα stages. In the secondary structure stage, helices and strands are identified with pre-computed templates, and the voxel size of the entire map is then refined to account for microscopic magnification errors. The identified secondary structures are then extended from both ends in the Cα stage via a log-likelihood (LLK) target function, and if possible, the side chains are also assigned. This program can build models of large proteins (~1 MDa) in a reasonable amount of time (~1 day) and thus has the potential to greatly decrease the manual workload required for model building of high-resolution cryoEM maps.
Highlights
In recent years, substantial progress has been made in single-particle analysis (SPA) and has led to a resolution revolution in cryo-electron microscopy[1]
Cα root-mean-square deviations (RMSDs) values were calculated by measuring the distance between each Cα in the model and the nearest Cα in the final structure deposited in the Protein Data Bank (PDB)
We developed EMBuilder, which uses a template-matching method for model building of cryo-electron microscopy (cryoEM) maps
Summary
Substantial progress has been made in single-particle analysis (SPA) and has led to a resolution revolution in cryo-electron microscopy (cryoEM)[1]. Automatic Crystallographic Map Interpreter (ACMI)[16] uses probabilistic inference to predict the backbone layout and a statistical sampling method to produce an accurate and physically feasible set of structures and side chain templates to sample side chains. All of these programs were developed to address the problem of model building specific in crystallography. The refinement procedure improves the phases of crystallographic maps iteratively, but no phase problem exists in cryoEM maps These distinct characteristics of cryoEM maps should stimulate the development of novel model-building programs for high-resolution cryoEM maps. We present a dedicated program—EMBuilder—based on the template-matching method for model building designed for high-resolution cryoEM maps
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