Molecule of the Month: Broadly Neutralizing Antibodies

Structural studies of broadly neutralizing antibodies are paving the way to vaccines for HIV, influenza and RSV

The Fab portion of a broadly-neutralizing antibody (blue) bound to HIV envelope glycoprotein (yellow, orange, and red).
The Fab portion of a broadly-neutralizing antibody (blue) bound to HIV envelope glycoprotein (yellow, orange, and red).
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Viruses like HIV and influenza have evolved sneaky methods for evading our immune system. The immune system searches for foreign molecules, but several viruses have found ways to hide their unique parts and masquerade as normal human molecules. They do this in many ways. As viral surface glycoproteins are synthesized in infected cells, they are decorated with the same sugar chains that coat human proteins, providing an effective camouflage. The conserved functional sites of the viral protein are hidden deep in a pocket surrounded by these sugars, and thus are difficult for antibodies to reach. In addition, these viruses have error-prone replication machinery, which creates a great diversity in the viral glycoproteins. So unfortunately, once the immune system has found antibodies to recognize the infecting virus, other viruses rapidly mutate to change the site that is recognized.

The Immune System Fights Back

Antibodies of the immune system tend to focus on easily accessible loops on the viral surface, which often have great sequence and conformational variability. This is a problem for two reasons: the virus population can quickly evade these antibodies, and the antibodies are attacking portions of the protein that are not essential for function. Amazingly, however, after several years of battle with the infection, some people develop broadly neutralizing antibodies, termed "broadly" because they attack many strains of the virus, and "neutralizing" because they attack key functional sites in the virus and block infection. Unfortunately, however, these antibodies usually come too late and do not provide effective protection from the disease.

Attacking HIV

Researchers are studying these broadly neutralizing antibodies and trying to find ways to spur the immune system into creating them quickly with a vaccine. Because they recognize unusual targets, they are unusual antibodies. The one shown here, from PDB entry 4nco , uses an approach seen in many of these antibodies. The structure includes one Fab arm of the antibody (in blue) and the outer portion of the HIV envelope glycoprotein (in yellow and red, with sugars in orange). The antibody has an unusually long extension of one of the loops, which pokes like a finger through the coating of sugar chains and into a conserved site of the viral glycoprotein. The rest of the antibody also has dozens of mutations that refine the interaction with surrounding protein and sugars.

Fab portions of three broadly-neutralizing antibodies (blue) bound to influenza hemagglutinin (yellow, orange, and red).
Fab portions of three broadly-neutralizing antibodies (blue) bound to influenza hemagglutinin (yellow, orange, and red).
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Attacking Influenza

Broadly neutralizing antibodies for influenza also focus on conserved functional targets, attacking a vulnerable site on the viral protein hemagglutinin . The one at the top uses a similar approach as the HIV-binding antibody, with a loop that extends into the receptor binding site. The two at the bottom attack another conserved function of the hemagglutinin: the machinery involved in membrane fusion. Structures for these three antibodies are available in PDB entries 3sm5 , 4fqi and 3sdy , and are shown all bound to one hemagglutinin in this illustration.

Exploring the Structure

RSV Vaccine Design (PDB entries 4jhw and 4mmv)

The ultimate goal of this research is to find way to make vaccines that will spur production of these broadly neutralizing antibodies, to provide protection against infection. Remarkably, this goal of structure-based vaccine design has been achieved for respiratory syncytial virus (RSV). The work started with a structure of a particularly potent antibody that neutralizes the receptor-binding site of the viral fusion glycoprotein, shown here on the left (PDB entry 4jhw ). Based on this structure, researchers engineered a soluble form of the glycoprotein that adopts the same shape as the antibody-bound form, requiring a number of mutations, shown here on the right (PDB entry 4mmv ). When mice and macaques are vaccinated with this engineered protein, it provides immunity from the virus. To explore these proteins in more detail, click on the image for an interactive Jmol.

Topics for Further Discussion

  1. PDB entry 1op5 includes an unusual domain-swapped antibody, which creates a third binding site in addition to the two conventional binding sites on the two Fab domains. It is a broadly neutralizing antibody that attacks the sugars on the surface of HIV envelope glycoprotein.
  2. Because they are so flexible, crystallographers typically study a fragment of antibodies which includes only one of the Fab arms. To see the structure of some intact antibodies, look at the examples in the Molecule of the Month on antibodies.


  1. 4nco: J. P. Julien, A. Cupo, D. Sok, R. L. Stanfield, D. Lyumkis, M. C. Deller, P. J. Klasse, D. R. Burton, R. W. Sanders, J. P. Moore, A. B. Ward & I. A. Wilson (2013) Crystal structure of soluble cleaved HIV-1 envelope trimer. Science 342, 1477-1483.
  2. 4mmv: J. S. McLellan, M. Chen, M. G. Joyce, M. Sastry, G. B. E. Stewart-Jones, Y. Yang, B. Zhang, L. Chen, S. Srivatsan, A. Zheng, T. Zhou, K. W. Graepel, A. Kumar, S. Moin, J. C. Boyington, G. Y. Chuang, C. Soto, U. Baxa, A. Q. Bakker, H. Spits, T. Beaumont, Z. Zheng, N. Xia, S. Y. Ko, J. P. Todd, S. Rao, B. S. Graham & P. D. Kwong (2013) Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus. Science 342, 592-598.
  3. 4jhw: J. S. McLellan, M. Chen, S. Leung, K. W. Graepel, X. Du, Y. Yang, T. Zhou, U. Baxa, E. Yasuda, T. Beaumont, A. Kumar, K. Modjarrad, Z. Zheng, M. Zhao, N. Xia, P. D. Kwong & B. S. Graham (2013) Structure of RSV fusion glycoprotein trimer bound to a prefusion-specific neutralizing antibody. Science 340, 1113-1117.
  4. 4fqi: C. Dreyfus, N. S. Laursen, T. Kwaks, D. Zuijdgeest, R. Khayat, D. C. Ekiert, J. H. Lee, Z. Metlagel, M. V. Bujny, M. Jongeneelen, R. van der Vlugt, M. Lamrani, H. J. W. M. Korse, E. Geelen, O. Sahin, M. Sieuwerts, J. P. Brakenhoff, R. Vogels, O. T. W. Li, L. L. Poon, M. Peiris, W. Koudstaal, A. B. Ward, I. A. Wilson, J. Goudsmit & R. H. Rriesen (2012) Highly conserved protective epitopes on influenza B viruses. Science 337, 1343-1348.
  5. J. P. Julien, P. S. Lee & I. A. Wilson (2012) Structural insights into key sites of vulnerability on HIV-1 Env and influenza HA. Immunological Reviews 250, 180-198.
  6. 3sdy: D. C. Ekiert, R. H. Friesen, G. Bhabha, T. Kwaks, M. Jongeneelen, W. Yu, C. Ophorst, F. Cox, H. J. W. M. Korse, B. Brandenberg, R. Vogels, J. P. Brakenhoff, R. Kompier, M. J. Koldijk, L. A. Cornelissen, L. L. Poon, M. Peiris, W. Koudstaal, I. A. Wilson & J. Goudsmit (2011) A highly conserved neutralizing epitope on group 2 influenza A viruses. Science 333, 843-850.
  7. 3sm5: J. R. Whittle, R. Zhang, S. Khurana, L. R. King, J. Manischewitz, H. Golding, P. R. Dormitzer, B. F. Haynes, E. B. Walter, M. A. Moody, T. B. Kepler, H. X. Liao & S. C. Harrison (2011) Broadly neutralizing human antibody that recognizes the receptor- binding pocket of influenza virus hemagglutinin. Proceedings of the National Academy of Science USA 108, 14216-14221.

February 2014, 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