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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...

Antibody Structure and Classes

Antibody Structure and Classes

Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.

Diversity of Antigen Receptors

Diversity of Antigen Receptors

Antigen receptors are essential components of the immune system crucial in defending the body against foreign invaders. These receptors are present on the surface of B and T cells, enabling them to recognize antigens and mount an appropriate immune response.
Before encountering any antigen, lymphocytes express these receptors. On B cells, the antigen receptor is a membrane-bound antibody molecule called BCR; on T cells, it is a T cell receptor or TCR. B and T cell receptors are composed of two...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Affinity and Avidity

Affinity and Avidity

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Selection of Transporter-Targeted Inhibitory Nanobodies by Solid-Supported-Membrane SSM-Based Electrophysiology

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Species-Dependent Structural Variations in Single-Domain Antibodies.

Marta Baselga¹, Javier Sánchez-Prieto¹, Víctor Manuel Medina Pérez¹

¹Institute for Health Research Aragon (IIS Aragón), 50009 Zaragoza, Spain.

Antibodies (Basel, Switzerland)

|December 24, 2025

Summary

Single-domain antibodies (sdAbs) from various camelids show conserved frameworks but variable loops, impacting engineering. The MO-IISA database captures these species-specific adaptations for improved antibody design.

Keywords:

Bactrian camels VHHs alpacas database dromedary camels llamas nanobody single-domain antibody fragments species-dependent

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Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

Published on: August 15, 2014

Area of Science:

Biotechnology
Immunology
Structural Biology

Background:

Single-domain antibodies (sdAbs) are derived from camelid heavy-chain antibodies (HCAb).
sdAbs offer advantages like small size, high stability, and ease of production, making them valuable for biomedical research and therapeutics.
While numerous sdAb structures are documented, comprehensive analyses of species-dependent structural variations are limited.

Purpose of the Study:

To evaluate species-dependent structural differences in single-domain antibodies (sdAbs).
To create a comprehensive, open-access database of sdAbs with known antigen targets.

Main Methods:

Assembled MO-IISA, an open-access database, by integrating six public resources (iCAN, INDI, SAbDab-nano, sdAb-DB, PLabDab-nano, NbThermo).
Applied harmonized eligibility criteria for data inclusion.
Quantified region lengths, amino acid frequency, and conservation/entropy across frameworks (FR1-FR4) for 2053 sdAbs.

Main Results:

The dataset included 2053 sdAbs from llamas (n=1316), alpacas (n=325), dromedary camels (n=377), and Bactrian camels (n=35).
Average sdAb length was ~124 amino acids with minor interspecies variations.
Framework regions (FRs) were highly conserved, while CDR2 and CDR3 exhibited the most inter- and intra-species variability. Lysine enrichment was noted in FR3 and FR2, and cysteines in FR1 and FR3, with non-canonical cysteines more frequent in Bactrian and dromedary sdAbs.

Conclusions:

Framework regions exhibit species-neutral constraints, while loop regions show species-tuned adaptations.
These structural features have practical implications for sdAb engineering, species selection, and conjugation strategies.
The MO-IISA database provides a valuable resource for exploring these species-specific characteristics in sdAbs.