Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure.

José L. Carrascosa,Rosa Pérez-Luque,Cristina Machón,Francisco J. Fernández,M. Cristina Vega,Ana Cuervo,Miquel Coll,Joan Pous,Montserrat Fàbrega-Ferrer

doi:10.1107/s2059798320015156

José L. Carrascosa, Rosa Pérez-Luque + Show 7 more

Open Access

https://doi.org/10.1107/s2059798320015156

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Abstract

Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallographic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-modification procedures using rotation matrices and a mask based on the cryo-EM structure were critical for solving the structure. A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-EM map for molecular replacement.

Highlights

X-ray crystallography is the technique that has provided the most high-resolution information in the field of structural biology
A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-electron microscopy (cryo-EM) map for molecular replacement
We show a case example in which a combination of the X-ray crystallography and cryo-EM techniques can be used in a different way, using a partial cryo-EM atomic model instead of the cryo-EM map for molecular replacement (MR)

Summary

Introduction

X-ray crystallography is the technique that has provided the most high-resolution information in the field of structural biology. The structural study of viral capsids with icosahedral symmetry, in which intermediate-resolution cryo-EM reconstructions were used as phasing models, has contributed significant methodological advances (Stuart & Abrescia, 2013). This approach takes advantage of the icosahedral symmetry present in the samples and uses symmetrized maps. After the cryo-EM resolution revolution, similar procedures applicable to samples without such high orders of symmetry have been developed (Xiong, 2008; Jackson et al, 2015; Zeng et al, 2018) In these approaches, the cryo-EM map was used directly as an initial model for density modification. The portal protein of the T7 bacteriophage is coded by the gp gene and has a predicted molecular weight of 59 kDa, which would give a multimeric complex of 650– 770 kDa, depending on its oligomerization state

Crystallization

Data collection and analysis

Structure solution

Using a medium-resolution cryo-EM map to obtain an initial model

Molecular replacement

Density modification and model building

Comparison with the direct use of a cryo-EM map for MR

Solution of the physiological dodecameric gp8 atomic model

Discussion

Findings

Conclusions

Funding information