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...
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...
Assembly of Cytoskeletal Filaments01:18

Assembly of Cytoskeletal Filaments

Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
Assembly of Complex Microtubule Structures01:32

Assembly of Complex Microtubule Structures

Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Studying the Cytoskeleton01:17

Studying the Cytoskeleton

The cytoskeletal architecture can be studied using different microscopic and biochemical techniques. Electron microscopy was instrumental in discovering the cytoskeletal architecture around the 1960s, which allowed obtaining structural information at a high-resolution level. However, the sample preparation procedure often limits this ability in biological samples. Several protocols have been developed over the years to optimize sample preparation. In one of the protocols known as rotary...

You might also read

Related Articles

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

Sort by
Same author

Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets.

bioRxiv : the preprint server for biology·2026
Same author

Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells.

Cell·2026
Same author

The scientific legacy of Martin Karplus from the perspective of his collaborators.

Biophysical journal·2026
Same author

The filamentous ultrastructure of the PopZ condensate is required for its cellular function.

Nature structural & molecular biology·2026
Same author

ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models.

Journal of molecular biology·2026
Same author

IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.

Journal of molecular biology·2025
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: May 25, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Macromolecular assembly structures by comparative modeling and electron microscopy.

Keren Lasker1, Javier A Velázquez-Muriel, Benjamin M Webb

  • 1Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA. kerenl@salilab.org

Methods in Molecular Biology (Clifton, N.J.)
|February 11, 2012
PubMed
Summary
This summary is machine-generated.

Electron microscopy (EM) advances enable high-resolution biological structure determination. This work details density map-guided comparative modeling to fit atomic models into EM maps, using tools like IMP and MODELLER.

More Related Videos

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Related Experiment Videos

Last Updated: May 25, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering
07:19

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • High-resolution structure determination of large biological assemblies is crucial for understanding cellular mechanisms.
  • Electron microscopy (EM) provides low-resolution density maps of these assemblies.
  • Fitting atomic models of components into EM maps is a key challenge.

Purpose of the Study:

  • To describe density map-guided comparative modeling approaches for atomic model fitting into EM maps.
  • To outline protocols for addressing various modeling problems constrained by EM density data.
  • To provide practical instructions for using specific software tools for this integrative modeling process.

Main Methods:

  • Comparative modeling techniques including fold assignment, sequence-structure alignment, model building, and assessment.
  • Integration of electron microscopy (EM) density maps to guide and restrain the modeling process.
  • Utilizing software platforms such as the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera.

Main Results:

  • Demonstration of how density map information can enhance each stage of comparative modeling.
  • Presentation of diverse modeling scenarios and corresponding solution protocols.
  • Detailed guidance on applying IMP, MODELLER, and UCSF Chimera for density map-guided modeling.

Conclusions:

  • Density map-guided comparative modeling is an effective strategy for atomic model building in structural biology.
  • The described protocols and tools facilitate the integration of EM data with computational modeling.
  • This approach aids in the accurate structure determination of large biological machines.