Em Density Map
Em Density Map - Related Videos
10:57
Mapping Absolute DNA Density in Cell Nuclei using Single-molecule Localization Microscopy
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2025
The present protocol describes a method measuring absolute DNA densities within adherent cell nuclei using Voronoi tessellation of single-molecule localization microscopy data, known volume, genome size, and cell cycle stage.
05:05
Preparation of High-Temperature Sample Grids for Cryo-EM
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Cited by 5 •
2021
This paper provides a detailed protocol for preparing sample grids at temperatures as high as 70 °C, prior to plunge freezing for cryo-EM experiments.
06:58
Fate Mapping
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2023
Fate mapping is a technique used to understand how embryonic cells divide, differentiate, and migrate during development. In classic fate mapping experiments, cells in different areas of an embryo are labeled with a chemical dye and then tracked to determine which tissues or structures they form. Technological improvements now allow for individual cells to be marked and traced throughout embryonic development and adulthood. This video reviews the concepts behind fate mapping, and then details a...
11:03
Motor Maps
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2023
Source: Laboratories of Jonas T. Kaplan and Sarah I. Gimbel—University of Southern California One principle of brain organization is the topographic mapping of information. Especially in sensory and motor cortices, adjacent regions of the brain tend to represent information from adjacent parts of the body, resulting in maps of the body expressed on the surface of the brain. The primary sensory and motor maps in the brain surround a prominent sulcus known as the central sulcus. The cortex...
08:01
Visualizing Proteins and Macromolecular Complexes by Negative Stain EM: from Grid Preparation to Image Acquisition
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Cited by 137 •
2011
Visualizing protein samples by negative stain electron microscopy (EM) has become a popular structural analysis method. It is useful for quantitative structural analysis, such as calculating a 3D reconstruction of the molecules being studied, and also for qualitative examination of the quality of protein preparations. In this article we present detailed protocols for preparing the EM grids, staining the sample and visualizing the sample in an electron microscope. Novice users can follow these...
FAQs
In cryo-electron microscopy, researchers begin with many two-dimensional particle images. They align these views so corresponding molecular orientations and features can be compared, then computationally combine them to estimate a three-dimensional volume. This reconstruction converts a collection of projections into a map that can be examined for the shape and organization of a biomolecular assembly.
Within a reconstructed volume, stronger density generally indicates the presence of protein, nucleic acid, or other macromolecular material. This intensity pattern helps researchers interpret where molecular components are located and how they are organized. The map therefore provides spatial information about composition and arrangement, rather than serving only as an image of an isolated feature.
Once a map has been reconstructed, biochemists can fit an atomic model into its features and refine that model using the map. This step links the experimental reconstruction to a more detailed molecular description, helping researchers analyze how particular structural elements are arranged within a protein, nucleic-acid-containing assembly, or larger complex.
Binding-site analysis uses the spatial features of an EM density map to examine where a ligand may be located within a biomolecular structure. Identifying such a site allows researchers to relate ligand placement to the surrounding molecular organization. This application is useful when the goal is to connect structural observations with biochemical questions about molecular interactions.
Maps can be used to examine conformational changes, meaning differences in molecular shape or organization between structural states. By studying these changes, biochemists can investigate how a biomolecule or complex rearranges and then relate that structural behavior to its function. This makes the map relevant to mechanistic studies rather than only to static structural description.
A two-dimensional particle image shows a view of a molecular specimen, whereas the reconstructed three-dimensional map represents the molecule's shape and organization in volume. Combining aligned images therefore gives biochemists a spatial framework for interpreting components and complexes, and for connecting observed structure with biochemical function.