Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Electron Microscope Tomography and Single-particle Reconstruction01:07

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
IR Frequency Region: Fingerprint Region01:03

IR Frequency Region: Fingerprint Region

IR spectra are divided into two main regions: the diagnostic region and the fingerprint region. The diagnostic region of the spectrum lies above 1500 cm−1. The absorptions resulting from single-bond vibrations of the N–H, C–H, and O–H stretch at higher wavenumbers and appear on the left side of the spectrum. The stretching absorptions of the C≡C and C≡N occur between 2100–2300 cm−1. In contrast, those arising from stretching absorptions of the C=O, C=N, and C=C occur between 1600–1850 cm−1.
The...
Scanning Electron Microscopy01:07

Scanning Electron Microscopy

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.
Fundamental Principles
Accelerated...
Cryo-electron Microscopy01:28

Cryo-electron Microscopy

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Reconstruction of septin higher-order nano-size structures in ovarian cancer cells uncover susceptibility to the septin-targeting small molecule UR214-9.

bioRxiv : the preprint server for biology·2026
Same author

Mechanistic role of APOE lipidation in Alzheimer's disease pathogenesis.

Theranostics·2026
Same author

Modular Deep Learning for Direct RNA Sequence Design via Self-Contained RNA Units.

bioRxiv : the preprint server for biology·2026
Same author

A diffusion-based framework for designing molecules in flexible protein pockets.

Science advances·2026
Same author

ChironRNA: Steric Clashes Resolution in RNA Structures via E(3)-Equivariant Diffusion.

bioRxiv : the preprint server for biology·2026
Same author

Unified protein-small molecule graph neural networks for binding site prediction.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

Related Experiment Video

Updated: Jun 4, 2026

Obtaining 3D Chemical Maps by Energy Filtered Transmission Electron Microscopy Tomography
08:15

Obtaining 3D Chemical Maps by Energy Filtered Transmission Electron Microscopy Tomography

Published on: June 9, 2018

Fingerprint-based structure retrieval using electron density.

Shuangye Yin1, Nikolay V Dokholyan

  • 1Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260, USA.

Proteins
|February 3, 2011
PubMed
Summary
This summary is machine-generated.

We developed a fast computational method using 3D Zernike moments to match protein structures with electron density maps from cryo-electron microscopy. This approach efficiently screens the Protein Data Bank for suitable structural fits.

More Related Videos

Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography
14:56

Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography

Published on: May 20, 2022

Microcrystal Electron Diffraction of Small Molecules
09:48

Microcrystal Electron Diffraction of Small Molecules

Published on: March 15, 2021

Related Experiment Videos

Last Updated: Jun 4, 2026

Obtaining 3D Chemical Maps by Energy Filtered Transmission Electron Microscopy Tomography
08:15

Obtaining 3D Chemical Maps by Energy Filtered Transmission Electron Microscopy Tomography

Published on: June 9, 2018

Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography
14:56

Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography

Published on: May 20, 2022

Microcrystal Electron Diffraction of Small Molecules
09:48

Microcrystal Electron Diffraction of Small Molecules

Published on: March 15, 2021

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Cryo-electron microscopy (cryo-EM) generates electron density maps crucial for determining protein structures.
  • Fitting atomic models to experimental electron density maps can be computationally intensive.
  • Identifying suitable protein structures from large databases is essential for structural biology research.

Purpose of the Study:

  • To present a novel computational approach for rapidly identifying protein structures that match given electron density maps.
  • To reduce the complexity of fitting structures to electron density data through a fingerprint comparison method.

Main Methods:

  • Utilizing geometric invariants, specifically 3D Zernike moments, to create descriptive fingerprints of electron density.
  • Developing a method to compare these fingerprints for efficient database searching.
  • Screening the entire Protein Data Bank (PDB) using the developed computational approach.

Main Results:

  • Demonstrated the ability to quickly search large protein structural databases.
  • Successfully identified protein structures that fit two experimental electron density maps obtained via cryo-electron microscopy.
  • The fingerprint comparison significantly simplifies the structure-fitting problem.

Conclusions:

  • The proposed computational approach offers an efficient and rapid method for fitting protein structures to electron density data.
  • This technique can be applied to large-scale database searches, aiding in structural determination from cryo-EM data.
  • Geometric invariants provide a powerful tool for comparing structural and density information in structural biology.