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5 Mar 2013

Structure and accessibility of HA trimers on intact 2009 H1N1 pandemic influenza virus to stem region-specific neutralizing antibodies (Proc Natl Acad Sci USA, abstract, edited)

[Source: Proceedings of the National Academy of Sciences of the United States of America, full text: (LINK). Abstract, edited.]

Structure and accessibility of HA trimers on intact 2009 H1N1 pandemic influenza virus to stem region-specific neutralizing antibodies

Audray K. Harrisa,1, Joel R. Meyersona,b,1, Yumiko Matsuokac, Oleg Kuybedad,e, Amy Morand, Donald Blissd, Suman R. Dasf, Jonathan W. Yewdellf, Guillermo Sapiroe,2, Kanta Subbaraoc, and Sriram Subramaniama,3

Author Affiliations: aLaboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Laboratories of cInfectious Diseases and fViral Diseases, National Institutes of Allergy and Infectious Diseases, and dNational Library of Medicine, National Institutes of Health, Bethesda, MD 20892; bMitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, United Kingdom; and eDepartment of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN 55455

Edited by Peter Palese, Mount Sinai School of Medicine, New York, NY, and approved January 23, 2013 (received for review August 28, 2012)



Rapid antigenic variation of HA, the major virion surface protein of influenza A virus, remains the principal challenge to the development of broader and more effective vaccines. Some regions of HA, such as the stem region proximal to the viral membrane, are nevertheless highly conserved across strains and among most subtypes. A fundamental question in vaccine design is the extent to which HA stem regions on the surface of the virus are accessible to broadly neutralizing antibodies. Here we report 3D structures derived from cryoelectron tomography of HA on intact 2009 H1N1 pandemic virions in the presence and absence of the antibody C179, which neutralizes viruses expressing a broad range of HA subtypes, including H1, H2, H5, H6, and H9. By fitting previously derived crystallographic structures of trimeric HA into the density maps, we deduced the locations of the molecular surfaces of HA involved in interaction with C179. Using computational methods to distinguish individual unliganded HA trimers from those that have bound C179 antibody, we demonstrate that ∼75% of HA trimers on the surface of the virus have C179 bound to the stem domain. Thus, despite their close packing on the viral membrane, the majority of HA trimers on intact virions are available to bind anti-stem antibodies that target conserved HA epitopes, establishing the feasibility of universal influenza vaccines that elicit such antibodies.

envelope glycoproteins  - subvolume averaging - virus structure  - hemagglutunin - cryo-electron microscopy



1A.K.H. and J.R.M. contributed equally to this work.

2Present address: Department of Electrical and Computer Engineering, Pratt School of Engineering, Duke University, Durham, NC 27708.

3To whom correspondence should be addressed. E-mail:

Author contributions: A.K.H. and S.S. designed research; A.K.H., J.R.M., and Y.M. performed research; O.K., S.R.D., J.W.Y., G.S., and K.S. contributed new reagents/analytic tools; A.K.H., J.R.M., O.K., A.M., D.B., and S.S. analyzed data; and A.K.H., J.R.M., and S.S. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at

Freely available online through the PNAS open access option.