An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains.

Lin Chen,Jing He,Rayshawn Walker,Salim Sazzed

doi:10.3390/molecules23030610

Lin Chen, Jing He + Show 2 more

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https://doi.org/10.3390/molecules23030610

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Abstract

Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2–4 Å resolutions. The results show that the normalized probability density function of block lengths is similar between the X-ray data set and the cryo-EM data set for most of the residue types, but differences were observed for ARG, GLU, ILE, LYS, PHE, TRP, and TYR for which conformations with certain shorter block lengths are more likely to be observed in the cryo-EM set with 2–4 Å resolutions.

Highlights

Cryo-electron microscopy is an emerging structure determination technique in addition to two other techniques: X-ray crystallography (X-ray) and Nuclear Magnetic Resonance (NMR).Currently, over 1900 atomic structures have been derived from electron density maps produced using cryo-EM technique, and they are deposited in Protein Data Bank (PDB) [1]
Over 1900 atomic structures have been derived from electron density maps produced using cryo-EM technique, and they are deposited in Protein Data Bank (PDB) [1]
We present a statistical analysis of structures derived from ultra-high-resolution density maps of X-ray and those derived from EM density maps with 2–4 Å resolutions

Summary

Introduction

Cryo-electron microscopy (cryo-EM) is an emerging structure determination technique in addition to two other techniques: X-ray crystallography (X-ray) and Nuclear Magnetic Resonance (NMR). Over 1900 atomic structures have been derived from electron density maps produced using cryo-EM technique, and they are deposited in Protein Data Bank (PDB) [1]. Some of the atomic structures are derived from cryo-EM density maps with 2–4 Å resolutions. Others are obtained from density maps of much lower resolutions. It is generally expected that atomic structures that are derived from high-quality density maps are more accurate than those derived from lower-quality maps. There are more than 5700 EM density maps in the EM Data Bank (EMDB) as of January 2018, about 54% of them have resolution lower than 10 Å and 24% with 5–10 Å resolution [2]

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