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Guide to Understanding PDB Data

Molecular Models: Exploring the Structure of an Antibody

In this activity you will make a paper model of an Immunoglobin G (IgG) antibody, a molecule that plays a critical role in our immune response to pathogens. This antibody molecule has 4 protein chains and 12 domains, so the activity may be best done as a group or class project. Completing parts of the activity as homework may facilitate assembling the antibody in class in a timely manner, which can be followed by discussions.

To learn further details about the structure and function of this molecule, you can compare the paper model to an atomic model of antibody displayed in the online interactive views included here.

The activity is presented in 3 sections:

  1. About antibodies - Introduction and some interesting facts
  2. Build a paper model of antibody IgG - Template and instructions for making the paper model
  3. Explore the atomic structure of antibody IgG - Interactive display of the atomic structure of an antibody and details about how its structure relates to its function

1. About Antibodies

Antibodies are proteins that recognize and bind to foreign objects in our body. They play a central role in the immune system, by finding pathogens, such as viruses and bacteria, and targeting them for destruction. Antibodies have a distinctive Y-shape, and are composed of two heavy chains and two light chains. The antigen-binding sites are located at the tips of the two arms formed by heavy and light chain domains. For an introduction to the structure and functions of IgG, see the Molecule of the Month features on Antibodies.

Antibody Types:

In addition to IgG, humans and other mammals produce other types of antibodies, such as the IgM, IgA, IgD and IgE. The heavy chains of all these immunoglobulin molecules vary, leading to differences in the overall shape of the molecule. B-cells recognize invaders through interactions with specialized antibodies on their cell surface (IgM and IgD), and are activated to produce lots of soluble immunoglobulins (IgG) to fight the infection. IgA is secreted in the gut and respiratory tract, helping protect us from any infections there. Finally IgE is secreted by mast cells and is involved in allergies.

Binding Antigen:

The N-terminal domains of immunoglobulin heavy and light chains are variable - i.e. different in different antibodies. Antigens bind to specific pockets at the tips of these variable domains and interact with 6 loops (3 loops each from the heavy and light chains). These loops, called hypervariable loops, are responsible for the complementarity of the antigen-antibody interactions. Hence these hypervariable loops are also called complementarity determining regions (CDR). Subtle and/or major changes in these hypervariable loops of antibodies enables highly specific antigen-antibody interactions. The rest of the domains in the immunoglobulin chains are relatively conserved or constant.

Antibody Fragments:

Limited digestion with the protease, papain, chops the antibody into three fragments. Two identical fragments retain the antigen-binding activity and are called Fab fragments, for "Fragment antigen binding." The third fragment has no antigen-binding activity, but was found to crystallize readily, so is named the Fc fragment for "Fragment crystallizable." A number of polysaccharides are covalently linked to this region, providing it some order and rigidity. This fragment interacts with effector molecules and cells by binding to a cellular receptor called the Fc receptor.

Use in Research and Medicine:

Specificity of antigen antibody binding forms the basis for diagnostic tests for many infectious, inflammatory, and immune system diseases. To diagnose a disease, the presence of a specific antigen or antibody is recognized (for example in a blood or mucosa sample) by interacting it with its counterpart antibody or antigen, respectively. In some cases the antibody itself is used as a treatment, such as in the case of some specific cancers and rheumatoid arthritis. In these instances it is critical that the antibody that is administered is very pure, specific and only binds to the antigen of choice. These antibodies, called monoclonal antibodies, prevent cross-reaction with any other related proteins, avoiding side effects and complications.

In research too, antibodies play a very important role in localizing and labeling specific proteins/cells, and forming stable complexes that can be studied. Thus, antibodies are key components of the various diagnostics techniques such as Enzyme Linked Immune Sorbent Assay (ELISA), Western blots, immunofluorescence, etc.

Some broadly-neutralizing antibodies isolated from patients infected with viruses such as HIV and influenza are currently being studied to reverse engineer its antigen and ultimately develop new vaccines. To learn more about the structure and functions of antibody-like molecules, see the Molecule of the Month features on Broadly Neutralizing Antibodies.

Immunoglobulin-like Molecules in Nature:

Camels and sharks make simpler immunoglobulins that are composed of a single type of chain, termed "heavy-chain antibodies" since they do not have a light chain. As with IgG, two chains associate together to form a Y-shaped complex, with several domains forming the constant region in the stem, and a single variable domain forming the antigen-binding site on the arms. Nanobodies, also known as single-domain antibodies, are now engineered from this variable domain. They are much simpler to synthesize than typical two-chain Fab molecules, and are widely used in research and medicine.

To learn more about the structure and functions of antibody-like molecules, see the Molecule of the Month features on Nanobodies.


2. Build a Paper Model of an Antibody

Use this PDF to build a paper model of Antibody.


Template (PDF)

Folding Instructions

Follow the instructions in the slides demonstrating how to build this antibody model.

Observe in the Antibody paper model and Discuss:
  1. Multiple chains:
    • This model has 4 different chains - the light chains are colored in shades of blue, while the heavy chains in shades of red, orange and pink. As you build the model, can you identify the primary, secondary, tertiary and quaternary structures of the Antibody molecule?
  2. Disulfide bridges:
    • Each immunoglobulin domain has a disulfide bridge. When making the paper model notice how flexible the structure of each domain is, before and after attaching the disulfide link strip. What does this tell you about the function of the disulfide bridges?
    • Disulfide bonds are formed as a result of an oxidation reaction. In which cellular compartment do you think disulfide linkages of the immunoglobulin are formed? (Hint: It is not in the cytoplasm.)

Model limitations

  1. Overall the antibody paper model is quite flexible, even though each of the immunoglobulin domains, and the papain digested fragments (Fab and Fc) regions are well ordered. While the paper model's flexibility at the hinges is representative of the actual antibody structure, covalently linked sugars in the conserved, Fc region make it a little more rigid. The paper model does not include any linked sugars.

3. Explore the Atomic Structure of Antibody (IgG)

The atomic structure of antibody IgG can be visualized using coordinates from the Protein Data Bank. Here the structure from PDB entry 1igt is shown in a JSmol interactive view.

Antibody IgG (PDB entry 1igt)

color chains like paper model color variable loops green color Fab pink and Fc green color chains with rainbow colors

show entire antibody show only one light chain

In the JSmol default view the chains are colored similarly to the paper model. Two heavy and two light chains of antibody IgG are linked together by disulfide bonds (sulfur in yellow) to form a "Y-shaped" molecule. Both heavy and light chains of IgG have a repeated domain structure, aptly called the immunoglobulin domain or beta-sandwich, with 3-4 strands on one side and 4-5 strands on the other. This domain structure is often reused by nature in various other immune system molecules and receptors. Notice that a single disulfide bond stabilizes each of the immunoglobulin domains.

The antigen binding sites are on the tips of the two arms, surrounded by the six hypervariable loops. Use the button to color these loops green. You can also highlight the domain structure in the JSmol using the button to color the Fab pink and Fc green. The polysaccharides attached to the immunoglobulin are shown with atomic spheres in the JSmol.

While the overall structure of the many immunoglobulin domains are similar, closer examination of the IgG structure reveals that variable domains (that bind to the antigen) have additional strands and loops and are slightly different from the constant domains (that do not bind the antigen). Use the lower button on the JSmol to display a closeup of only one light chain. Notice that the variable domain (brighter colors in the model coloring scheme, or with green hypervariable loops in the coloring scheme that highlights them) has 4 and 5 beta strands in each sheet forming the beta-sandwich, but the constant domain has 4 and 3 strands.

Antibody Fab (PDB entries 1igt and 4nco)

color chains color variable loops green color chains with rainbow colors

show broadly-neutralizing Fab show typical Fab

As the name implies, the hypervariable loops are quite different when you compare different antibodies. The second JSmol compares two antibody Fab fragments--the one from the antibody shown above and one from a broadly-neutralizing antibody that is effective against HIV. The anti-HIV antibody was found to have an extra long loop when compared to other antibodies. Can you suggest a reason why this long loop provides an advantage?


Topics for further exploration

  1. How are antibodies made for use in research and medicine?
  2. How are monoclonal antibodies made?

References: (check formatting of refs).

  1. The structure of a typical antibody molecule from Immunobiology: The Immune System in Health and Disease. 5th edition. (http://www.ncbi.nlm.nih.gov/books/NBK27144/)
  2. Refined Structure of an Intact IgG2a Monoclonal Antibody, Biochemistry1997, 36, 1581-1597
  3. Nanobodies: Natural Single-Domain Antibodies; Annu. Rev. Biochem. 2013. 82:775-97
  4. Broadly neutralizing antibodies against HIV-1: templates for a vaccine. Virology. 2013 Jan 5; 435(1):46-56. doi: 10.1016/j.virol.2012.10.004.