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Antibody Structure

Antibody Structure

Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...

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Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope

Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope

Published on: March 24, 2017

IEDB-3D: structural data within the immune epitope database.

Julia Ponomarenko¹, Nikitas Papangelopoulos, Dirk M Zajonc

¹San Diego Supercomputer Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, CA 92093, USA. jpon@sdsc.edu

Nucleic Acids Research

|October 30, 2010

Summary

This summary is machine-generated.

IEDB-3D provides 3D structural data for immune epitopes, including B-cell and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands. This resource integrates curated and calculated structural information with functional assay data for comprehensive epitope research.

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Area of Science:

Immunology
Structural Biology
Bioinformatics

Background:

The Immune Epitope Database (IEDB) is a comprehensive resource for epitope data.
Access to 3D structural information of immune complexes is crucial for understanding epitope recognition.
Existing databases may not fully integrate structural data with immunological context.

Purpose of the Study:

To introduce IEDB-3D, the 3D structural component of the IEDB.
To catalog and provide access to 3D structures of epitope-MHC/antibody/TCR complexes.
To enable querying and visualization of structural and immunological data.

Main Methods:

Curating journal articles and Protein Data Bank (PDB) structures related to immune epitopes.
Calculating intermolecular contacts and interface areas for curated structures.
Integrating structural data with existing IEDB immunological and functional information.

Main Results:

IEDB-3D catalogs B-cell and T-cell epitopes and MHC ligands with available 3D structures in PDB.
Provides calculated structural data (contacts, interface areas) and visualization tools (EpitopeViewer).
Allows multi-faceted querying based on pathogen, immune response, and immune system components.

Conclusions:

IEDB-3D enhances the IEDB by providing integrated 3D structural data for immune epitopes.
Facilitates deeper understanding of epitope-antibody, epitope-TCR, and epitope-MHC interactions.
Offers comprehensive data retrieval and download options for researchers.