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Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120

Nature Structural & Molecular Biology volume 20, pages 796–803 (2013)Cite this article

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Abstract

A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb PGT 135 binds its Asn332 glycan–dependent epitope from its 3.1-Å crystal structure with gp120, CD4 and Fab 17b. PGT 135 interacts with glycans at Asn332, Asn392 and Asn386, using long CDR loops H1 and H3 to penetrate the glycan shield and access the gp120 protein surface. EM reveals that PGT 135 can accommodate the conformational and chemical diversity of gp120 glycans by altering its angle of engagement. Combined structural studies of PGT 135, PGT 128 and 2G12 show that this Asn332-dependent antigenic region is highly accessible and much more extensive than initially appreciated, which allows for multiple binding modes and varied angles of approach; thereby it represents a supersite of vulnerability for antibody neutralization.

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Figure 1: Crystal structure of PGT 135 in complex with HIV-1 gp120 core.
Figure 2: PGT 135 neutralization and binding.
Figure 3: Glycan dependency of PGT 135 binding to gp120.
Figure 4: A gp140 trimer binds Fab PGT 135 in slightly different orientations, in contrast to PGT 128, which is bound in a single orientation.
Figure 5: Supersite of vulnerability centered on the Asn332 glycan.
Figure 6: Conserved conformation of Asn332 glycan.

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Acknowledgements

We thank X. Dai for help with data processing; J. Chittuluru for assistance with the 2D PCA; D. Ekiert for initial cloning of PGT 135; R. Pejchal for initial cloning of soluble CD4 and the gp120 JR-FL core construct; C. Poulsen and R. Wyatt from The Scripps Research Institute, La Jolla, California, USA for donation of 17b IgG; C. Arnold from the UK National Institute for Biological Standards and Control, Health Protection Agency for donation of ARP3119 monoclonal antibody CA13; M. Elsliger for computer support; C. Corbaci for help with preparing figures and movies; A. Irimia, C. Blattner and M. Hong for discussions; J.P. Verenini for help in manuscript formatting; and W. Koff for discussions and support. We also thank S.C. Arzberger from ADA Technologies (Littleton, Colorado, USA), J. Zhang, currently at Life Bioscience (Aurora, Colorado, USA), and ADA Technologies for supplying the high-density NHS-activated slides used for glycan microarray analysis; members of the Glycosciences Laboratory for their collaboration in the establishment of the neoglycolipid-based microarray system; and T. Butters and colleagues from the University of Oxford, Oxford, UK for the glucosylated N-glycans. Work using the neoglycolipid system is supported by the Wellcome Trust (WT093378MA and WT099197MA) (T.F.), the UK Research Councils' Basic Technology Initiative 'Glycoarrays' (GRS/79268) (T.F.), UK Engineering and Physical Sciences Research Council Translational grant (EP/G037604/1) and US National Cancer Institute (NCI) Alliance of Glycobiologists for Detection of Cancer and Cancer Risk (U01 CA128416) (T.F.). The EM data were collected at the US National Resource for Automated Molecular Microscopy, which is supported by the US National Institutes of Health (NIH) through the National Center for Research Resources' P41 program (RR017573) at the National Center for Research Resources. X-ray data sets were collected at the Advanced Light Source beamline 5.0.2 at the Berkeley Center for Structural Biology (BCSB) and the Advanced Photon Source beamline 23ID-B. The BCSB is supported in part by the NIH, the NIH National Institute of General Medical Sciences (NIGMS) and the Howard Hughes Medical Institute. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences of the US Department of Energy (DOE) under contract no. DE-AC02-05CH11231. Use of the APS was supported by the DOE, Basic Energy Sciences, Office of Science, under contract no. DE-AC02-06CH11357. The GM/CA-CAT 23-ID-B beamline has been funded in whole or in part with federal funds from the NCI (Y1-CO-1020) and NIGMS (Y1-GM-1104). This work was supported by the International AIDS Vaccine Initiative Neutralizing Antibody Center; by the Center for HIV/AIDS Vaccine Immunology (CHAVI-ID UM1 AI100663) (A.B.W., D.R.B. and I.A.W.); by the HIV Vaccine Research and Design program (P01 AI82362 and R37 AI36082) (J.P.M., A.B.W. and I.A.W.); by the University of California, San Diego, Center for AIDS Research (A.B.W.), an NIH-funded program (P30 AI036214) supported by the following NIH institutes and centers: US National Institute of Allergy and Infectious Disease, NCI, US National Institute of Mental Health, US National Institute on Drug Abuse, US National Institute of Child Health and Human Development, US National Institute of Heart, Lung and Blood and US National Institute of Aging; by NIH RO1 grants AI84817 (I.A.W.) and AI33292 (D.R.B.); and by the Joint Center of Structural Genomics by the NIH NIGMS Protein Structure Initiative (U54 GM094586) (I.A.W.). A portion of this work was supported by an American Foundation for AIDS Research Mathilde Krim Fellowship in Basic Biomedical Research (L.K.). The content is the responsibility of the authors and does not necessarily reflect the official views of the NIGMS, NCI or NIH. This is manuscript #21722 from The Scripps Research Institute.

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Authors and Affiliations

  1. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA

    Leopold Kong, Jeong Hyun Lee, Charles D Murin, Jean-Philippe Julien, Yuanzi Hua, Reza Khayat, Marc C Deller, Thomas Clayton, Henry Tien, Robyn L Stanfield, Andrew B Ward & Ian A Wilson

  2. International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, USA

    Leopold Kong, Katie J Doores, Jean-Philippe Julien, Yuanzi Hua, Khoa M Le, Robyn L Stanfield, Dennis R Burton, Andrew B Ward & Ian A Wilson

  3. Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA

    Katie J Doores, Khoa M Le & Dennis R Burton

  4. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA

    Katie J Doores & Dennis R Burton

  5. Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, USA

    Ryan McBride & James C Paulson

  6. Department of Medicine, Glycosciences Laboratory, Imperial College London, London, UK

    Yan Liu & Ten Feizi

  7. Weill Medical College of Cornell University, New York, New York, USA

    Andre Marozsan, Albert Cupo, Per-Johan Klasse, Rogier W Sanders & John P Moore

  8. International AIDS Vaccine Initiative Design and Development Laboratory, Brooklyn, New York, USA

    Simon Hoffenberg, Michael Caulfield & C Richter King

  9. Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, California, USA

    Marc C Deller, Thomas Clayton & Henry Tien

  10. Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands

    Rogier W Sanders

  11. Scripps Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, The Scripps Research Institute, La Jolla, California, USA

    Dennis R Burton, Andrew B Ward & Ian A Wilson

  12. Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA

    Ian A Wilson

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  1. Leopold Kong
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Contributions

Project design by L.K., K.J.D., J.-P.J., R.L.S., D.R.B., A.B.W. and I.A.W.; X-ray experimental work by L.K., J.-P.J., Y.H. and R.L.S.; EM experimental work by J.H.L., C.D.M., R.K. and A.B.W.; glycan-array experimental work by R.M., J.C.P., Y.L. and T.F.; mutational experimental work by K.J.D. and K.M.L.; Env-trimer reagents from A.M., A.C., P.-J.K., S.H., M.C., C.R.K., R.W.S. and J.P.M.; robotic crystallization screening by M.C.D., T.C. and H.T.; manuscript written by L.K., J.H.L., K.J.D., R.L.S., J.P.M., D.R.B., A.B.W. and I.A.W. All authors were asked to comment on the manuscript.

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Correspondence to Dennis R Burton, Andrew B Ward or Ian A Wilson.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6, Supplementary Tables 1–10 and Supplementary Note (PDF 1528 kb)

Supplementary Movie 1

Morphs illustrating the flexible interaction between the SOSIP gp140 trimer and PGT 135. The movie was created using UCSF Chimera by morphing between the 2D class average top views of PGT135 and each of the first 5 eigenvectors (a-e) from 2D principal component analysis (PCA). The positions of the gp140 trimer, PGT 135 Fabs and important N-linked glycans (N332 and N386) are labeled for clarity. Each morph is looped six times in the movie. The morph between the class average and each eigenvector of the variance highlights the range of flexibility exhibited in the Fab-trimer interaction. The extent of the variance is reduced in each successive eigenvector. (QuickTime; 8.0 MB) (MOV 7840 kb)

Supplementary Movie 2

Morphs illustrating the interaction between the SOSIP gp140 trimer and PGT 128. The movie was created as in Supplementary Movie 1, depicting morphs from each of the first 5 eigenvectors (a-e) from the PCA. The positions of the gp140 trimer, PGT 128 Fabs and the glycan at N332 are labeled for clarity. Each morph is looped six times in the movie. Analysis of the PGT 128-trimer interaction was used as a control for comparison with the PGT 135 interaction. From these morphs, it is clear that the extent of variance for PGT 128 is substantially less than that for PGT 135. (QuickTime; 6.7 MB) (MOV 6553 kb)

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Kong, L., Lee, J., Doores, K. et al. Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120. Nat Struct Mol Biol 20, 796–803 (2013). https://doi.org/10.1038/nsmb.2594

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