The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP.

Victor S. Lamzin,Grzegorz Chojnowski,Egor Sobolev,Philipp Heuser

doi:10.1107/s2059798320016332

Abstract

Recent developments in cryogenic electron microscopy (cryo-EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high-resolution cryo-EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo-EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main-chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo-EM maps is comparable to that of X-ray crystallographic models at similar local cryo-EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.

Highlights

Unlike X-ray crystallography, cryogenic electron microscopy does not require crystalline specimens, which makes it well suited for studying large, structurally heterogeneous macromolecules that may be reluctant to crystallize (Nogales & Scheres, 2015)
We observed that the completeness of the ARP/wARP models built de novo into the test-set cryogenic electron microscopy (cryo-EM) maps correlates with the reported resolution, the spread is rather large (Fig. 1)
We have systematically evaluated the reliability of models automatically built into cryo-EM maps using ARP/ wARP

Summary

Introduction

Unlike X-ray crystallography, cryogenic electron microscopy (cryo-EM) does not require crystalline specimens, which makes it well suited for studying large, structurally heterogeneous macromolecules that may be reluctant to crystallize (Nogales & Scheres, 2015). Recent developments in detector technology and advances in data-processing algorithms have enabled cryo-EM maps to be obtained at resolutions only previously attainable using X-ray crystallography (Wlodawer et al, 2017). Even a high-resolution map needs to be interpreted in terms of an atomic model to be useful in explaining biological processes (Renaud et al, 2018). An accurate model can be built manually with the use of computer graphics, for example using Coot (Emsley et al, 2010). This, can be time-consuming, error-prone and require expert knowledge when the features of a three-dimensional map need to be interpreted visually. Objective, robust and automated approaches are urgently required, for the model building of large complexes

Methods

Results

Conclusion