Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy

Abstract

Cryo-electron microscopy (EM) and small angle X-ray scattering (SAXS) are two different data acquisition modalities often used to glean information about the structure of large biomolecular complexes in their native states. A SAXS experiment is generally considered fast and easy but unveils the structure at very low resolution, whereas a cryo-EM experiment needs more extensive preparation and postacquisition computation to yield a threedimensional (3D) density map at higher resolution. In certain applications, we may need to verify whether the data acquired in the SAXS and cryo-EM experiments correspond to the same structure (e.g., before reconstructing the 3D density map in EM). In this article, a simple and fast method is proposed to verify the compatibility of the SAXS and EM experimental data. The method is based on averaging the two-dimensional correlation of EM images and the Abel transform of the SAXS data. Orientational preferences are known to exist in cryo-EM experiments, and we also consider these effects on our method. The results are verified on simulations of conformational states of large biomolecular complexes.

A systematic review of chromogranin A (CgA) and its biomedical applications, unveiling its structure-related functions

“…The SAXS analysis suggested the formation of a filament represented as a monodisperse rod with a cylindrical radius of ~ 52 Å, which is consistent with the result from negative-stain electron microscopy, supporting the formation of a filament structure with a radius of 47 ± 2.3 Å [37]. Therefore, SAXS becomes more informative when combined with other complementary information obtained using the integrative approaches [93]. The global size and shape information obtained by using SAXS complements the local spatial information obtained by using NMR.…”

“…Density maps of target particles are obtained using electron microscopy (EM) through 3D reconstruction based on 2D class averages classified in random orientations [93,97,98]. The 3D density maps provide global size and shape information, which are further combined with other complementary information [99].…”

Need for Cross-Validation of Single Particle Cryo-EM

“…More recently, Kim et al 68 proposed a measure of the compatibility between cryo-EM particles and small-angle X-ray scattering data for cross-validation. However, the method is useful only in the low-resolution regime, and it does not assess cryo-EM reconstructions but only the consistency between the data from the two experiments.…”

Cross-Modal Fusion Between Data in SAXS and Cryo-EM for Biomolecular Structure Determination

“…SAXS is known for its relatively low resolution and low information content in comparison to cryo-EM. Nevertheless, the information provided in these methods can be used to complement each other provided that the structural features in both experimental conditions are compatible Kim et al [2017].…”