Secretory Antibodies

Secretory immunoglobulins are our most abundant antibodies, providing a first line of defense against pathogens.

This article was written and illustrated by Lauryn Brooks, Carolina Colón-Colón, Aayushi Patel and Asya Polat as part of a week-long boot camp for undergraduate and graduate students hosted by the Rutgers Institute for Quantitative Biomedicine.

Secretory IgA is shown with antigen-binding domains (Fab) in red, constant domains (Fc) in orange and yellow, J-chain in magenta, and secretory component in purple. The illustration includes two structures: an atomic structure of the core (6ue7) and a low-resolution structure for the Fab domains (3chn).
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Guardians of Biology

Not every antibody can fight every type of infection. When thinking of our immune system, we might think all battles are fought in our blood, but in fact, most of the antibodies we produce protect other parts of the body. These antibodies are known as secretory antibodies, and they are our first line of defense against mucosal pathogens. Two types, secretory immunoglobulins A (sIgA) and M (sIgM), play a major role in protecting the mucosal linings throughout the body. Amazingly, due to the large area of mucosal surfaces, we produce around 2-3 grams of these antibodies in our gut every day. These antibodies are essential to our immune response against mucosal pathogens like SARS-CoV-2 and intestinal bacteria. They also play a role in beneficial interactions with our commensal microbiome. Recently published research is showing that these friendly bacteria promote resistance to infection by competing with pathogenic bacteria for sites of colonization, producing inhibitory molecules, and preparing our immune defenses.

Getting a Firm Grip

Given their unique job, secretory antibodies have specialized structures that allow them to withstand the harsh environment of our lungs, stomach, small and large intestines, biliary system, and genitourinary tract. Secretory antibodies build on the classic Y-shaped structure of a typical antibodies, but add a few unique modifications that assist in their function. To assist with recognition of pathogens, secretory antibodies often include many arms: sIgA (shown here from PDB entries 3chn and 6ue7) is composed of two (or more) Y-shaped subunits, and sIgM has five Y-shaped subunits. These many arms allow them to bind simultaneously to many sites on a pathogen, strengthening the interaction. A special J-chain holds them together and short extensions at the end of the chains associate into a beta-sheet arrangement similar to an amyloid fiber to further stabilize the entire assembly.

Getting Out

Secretory antibodies rely on a specialized protein to deliver them to the proper place. In the endoplasmic reticulum and Golgi, the polymeric immunoglobulin receptor binds to the antibody and assists with export out of the cell. Once outside, the receptor protein is cleaved, releasing the antibody. The antibody-binding portion of the receptor, called the “secretory component,” remains bound to the antibody, as seen in the structure shown here.

Complex of the bacterial protease (sIgA1P, with domains colored shades of blue) with a portion of a secretory IgA. Notice how the linker between the Fab and Fc regions of the antibody is stretched out and available for cleavage.
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Plotting Against the Guardians

Bacteria fight back against these secreted antibodies. For example, Streptococcus pneumonia, a bacterial pathogen that causes pneumonia and meningitis, secretes a protease (IgA1P) that inactivates antibodies by breaking them into pieces. As seen in PDB entry 6xja, it consists of three parts: a domain that binds to the antigen-binding (Fab) portion of the antibody, a domain that binds to the constant (Fc) portion of the antibody, and a protein-cutting active site in between. Intriguingly, these bacteria then use the Fab fragments as a protective coat to hide from the host’s immune system.

Exploring the Structure

Secretory IgM Core

Secretory IgM antibodies have five copies of the typical Y-shaped antibodies, allowing them to bind to many adjacent sites on the surface of a pathogen. As with sIgA, the complex is held together with a J-chain (magenta) and a beta-sheet of tails from the antibody chains (bright yellow). It also includes a secretory component, shown in purple. PDB entry 6kxs, shown here, includes the central core of the molecule, but is missing the Fab domains. To explore this structure in more detail, click on the image for an interactive Jsmol.

Topics for Further Discussion

  1. Learn more about the structures and functions of antibodies at PDB-101 by building a paper model.
  2. Secretory IgA also forms larger complexes, with more than two Y-shaped antibodies. To explore some of them, search for “secretory IgA” at the main RCSB PDB site.


  1. Bharathkar, S.K., Parker, B.W., Malyutin, A.G., Haloi, N., Huey-Tubman, K.E., Tajkhorshid, E., Stadtmueller, B.M. (2020) The structures of secretory and dimeric immunoglobulin A. eLife 9:e56098.
  2. 3chn: Bonner, A., Almogren, A., Furtado, P.B., Kerr, M.A., Perkins, S.J. (2009) Location of secretory component on the Fc edge of dimeric IgA1 reveals insight into the role of secretory IgA1 in mucosal immunity. Nature 2: 74-84.
  3. Chen, K., Magri, G., Grasset, E.K., Cerutti, A. (2020) Rethinking mucosal antibody responses: IgM, IgG and IgD join IgA. Nature Rev Immunol 20, 427-441.
  4. 6ue7: Kumar, N., Arthur, C. P., Ciferri, C., Matsumoto, M. L. (2020) Structure of the secretory immunoglobulin A core. Science 367: 1008-1014.
  5. Kumar, N., Arthur, C. P., Ciferri, C., Matsumoto, M. L. (2021) Structure of the human secretory immunoglobulin M core. Structure 29: 564-571.
  6. 6kxs: Li, Y., Wang, G., Li, N., Wang, Y., Zhu, Q., Chu, H., Wu, W., Tan, Y., Yu, F., Su, X-D., Gao, N., Xiao, J. (2020) Structural insights into immunoglobulin M. Science 367: 1014-1017.
  7. Seikrit, C., Pabst, O. (2021) The immune landscape of IgA induction in the gut. Semin Immunopathol 43: 627–637.
  8. Sterlin, D., Mathian, A., Miyara, M., Mohr, A., Anna, F., Claër, L., Quentric, P., Fadlallah, J., Devilliers, H., Ghillani, P., Gunn, C., Hockett, R., Mudumba, S., Guihot, A., Luyt, C-E., Mayaux, J., Beurton, A., Fourati, S., Bruel, T., Schwartz, O., Lacorte, J-M., Yssel, H., Parizot, C., Dorgham, K., Charneau, P., Amoura, Z., Gorochov, G. (2021) IgA dominates the early neutralizing antibody response to SARS-CoV-2. Science Transl Med 13: eabd2223.
  9. 6xja: Wang, Z., Rahkola, J., Redzic, J. S., Chi, Y. C., Tran, N., Holyoak, T., Zheng, H., Janoff, E., Eisenmesser, E. (2020) Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease. Nature Comm 11: 6063.
  10. Yang, Y., Palm, W. (2020). Immunoglobulin A and the microbiome. Curr Opin Microbiology 56: 89-96.

August 2022, Lauryn Brooks, Carolina Colón-Colón, Aayushi Patel, Asya Polat, David Goodsell

About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More