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Related Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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X-ray Crystallography02:18

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The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
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An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum...
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Overview of Electron Microscopy01:25

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The wavelengths of visible light ultimately limit the maximum theoretical resolution of images created by light microscopes. Most light microscopes can only magnify 1000X, and a few can magnify up to 1500X. Electrons, like electromagnetic radiation, can behave like waves, but with wavelengths of 0.005 nm, they produce significantly greater resolution up to 0.05 nm as compared to 500 nm for visible light. An electron microscope (EM) can create a sharp image that is magnified up to 2,000,000X.
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Scanning Electron Microscopy01:07

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A scanning electron microscope (SEM) is used to study the surface features of a sample by using an electron beam that scans the sample surface in a two-dimensional manner. Typically, areas between ~1 centimeter to 5 micrometers in width can be imaged. SEM can be used to image bacteria, viruses, tissues as well as larger samples like insects. Conventional SEM gives a magnification ranging from 20X to 30,000X and spatial resolution of 50 to 100 nanometers.
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Transmission Electron Microscopy01:15

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In 1931, physicist Ernst Ruska—building on the idea that magnetic fields can direct an electron beam just as lenses can direct a beam of light in an optical microscope—developed the first prototype of the electron microscope. This development led to the development of the field of electron microscopy. In the transmission electron microscope (TEM), electrons are produced by a hot tungsten element and accelerated by a potential difference in an electron gun, which gives them up to 400...
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Single Particle Cryo-Electron Microscopy: From Sample to Structure
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Single Particle Cryo-Electron Microscopy: From Sample to Structure

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Using cryo-electron microscopy maps for X-ray structure determination.

Lingxiao Zeng1, Wei Ding2, Quan Hao1,2

  • 1School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong.

Iucrj
|July 14, 2018
PubMed
Summary
This summary is machine-generated.

This study presents a hybrid method combining cryo-electron microscopy (cryo-EM) maps with X-ray crystallography to automate macromolecular structure determination. The approach successfully generates near-complete models from low-resolution cryo-EM data, advancing structural biology.

Keywords:
FSEARCHIPCASX-ray crystallographycryo-EMcryo-electron microscopyiterative phasingmodel buildingphase problemstructure determination

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Area of Science:

  • Structural Biology
  • Biophysics
  • Biochemistry

Background:

  • X-ray crystallography and cryo-electron microscopy (cryo-EM) are key techniques for determining macromolecular structures.
  • Crystallography offers high detail, while cryo-EM excels with large macromolecules.
  • Bridging the resolution gap allows cryo-EM maps to aid crystallography's phase problem.

Purpose of the Study:

  • To present a novel hybrid method integrating cryo-EM maps with X-ray crystallography for automated structure determination.
  • To demonstrate the utility of cryo-EM maps as starting points for solving the crystallographic phase problem.
  • To provide an automated workflow for generating complete macromolecular models.

Main Methods:

  • A three-step hybrid method was developed: (1) Cryo-EM map replacement using FSEARCH for orientation and translation within the unit cell.
  • (2) Phase extension from the cryo-EM map to high-resolution X-ray data using phenix.resolve and non-crystallographic symmetry averaging.
  • (3) Automated model building and completion using the Iterative Protein Crystal structure Automatic Solution (IPCAS) pipeline.

Main Results:

  • The hybrid method was successfully applied to four test cases, with the lowest cryo-EM map resolution at 6.9 Å.
  • Nearly complete macromolecular models were generated for all tested cases.
  • The resulting models exhibited reasonable Rwork/Rfree values, validating the method's accuracy.

Conclusions:

  • The developed hybrid method provides an automated and effective tool for X-ray structure determination.
  • Utilizing cryo-EM maps as starting points significantly streamlines the structure solution process.
  • This integrated approach enhances the capabilities of both cryo-EM and X-ray crystallography in structural biology.