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

Protein-protein Interfaces02:04

Protein-protein Interfaces

14.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.4K
Protein Organization01:24

Protein Organization

9.0K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
9.0K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

62.9K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
62.9K
Gene Families01:57

Gene Families

9.7K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
9.7K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.1K
2.1K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.8K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.8K

You might also read

Related Articles

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

Sort by
Same author

Towards globally equitable bioinformatics adoption.

PLoS biology·2026
Same author

Cybersecurity and Privacy Issues in Extended Reality Health Care Applications: Scoping Review.

JMIR XR and spatial computing·2026
Same author

PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search.

bioRxiv : the preprint server for biology·2026
Same author

Support needs assessment tool for people with disability wanting to participate in sport and exercise (SNAT-SE): Usability and acceptability testing.

JSAMS plus·2026
Same author

MolViewStories: Interactive molecular storytelling.

Protein science : a publication of the Protein Society·2026
Same author

Optimising communication function in primary brain tumour: a randomised controlled trial of CanCommunicate.

Disability and rehabilitation·2026
Same journal

Tesorai Search: cloud-based database search engine boosts identifications for mass spectrometry proteomics with a pretrained peptide-spectrum deep-learning model.

Journal of molecular biology·2026
Same journal

Characterization of diverse functions of NRF1 nuclear localization sequence.

Journal of molecular biology·2026
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
See all related articles

Related Experiment Video

Updated: Jan 7, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

14.8K

PDBe-KB Complexes: Enabling Functional Insight from Macromolecular Complexes in the PDB.

Sri Devan Appasamy1, Sreenath Nair1, Dare Kayode Lawal1

  • 1Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Journal of Molecular Biology
|December 28, 2025
PubMed
Summary
This summary is machine-generated.

PDBe-KB Complexes consolidates macromolecular assemblies from the Protein Data Bank (PDB) into unique records. This resource enables deeper analysis of complex structures, interactions, and functional diversity across life sciences.

Keywords:
PDBe-KBdata integrationmacromolecular complexesnucleic acidprotein

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.0K
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

13.2K

Related Experiment Videos

Last Updated: Jan 7, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
07:33

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

14.8K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.0K
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

13.2K

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Macromolecular assemblies are crucial for biological functions.
  • Existing databases often present assemblies in a fragmented manner.
  • A unified view of experimentally determined macromolecular assemblies is needed.

Purpose of the Study:

  • To create a comprehensive resource of unique macromolecular complex records.
  • To facilitate comparative and functional analyses of biological assemblies.
  • To provide a framework for understanding complex relationships and properties.

Main Methods:

  • Aggregation of experimentally determined macromolecular assemblies from the Protein Data Bank (PDB).
  • Creation of unique complex-level records within the PDBe-KB framework.
  • Comparison of complex compositions to establish relationships (subcomplexes, higher-order complexes).
  • Integration of component identity, stoichiometry, symmetry, ligands, and PISA-derived properties.

Main Results:

  • Over 100,000 unique complex compositions are now available.
  • Includes protein, nucleic acid, and mixed complexes.
  • Demonstrates utility with a case study of the SARS-CoV-2 spike protein complex, revealing conformational diversity and ligand interactions.
  • Enables analysis beyond traditional PDB entry-centric views.

Conclusions:

  • PDBe-KB Complexes offers a unified and comprehensive foundation for studying macromolecular assemblies.
  • Facilitates comparative analysis, supporting fundamental and translational research.
  • Enhances understanding of complex structures, interactions, and functional diversity.
  • Supports education and research across the life sciences.