Article | Published:

Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site

Nature Structural & Molecular Biology volume 23, pages 906915 (2016) | Download Citation

Abstract

HIV-1 vaccine design is informed by structural studies elucidating mechanisms by which broadly neutralizing antibodies (bNAbs) recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env). Variability in high-mannose and complex-type Env glycoforms leads to heterogeneity that usually precludes visualization of the native glycan shield. We present 3.5-Å- and 3.9-Å-resolution crystal structures of the HIV-1 Env trimer with fully processed and native glycosylation, revealing a glycan shield of high-mannose and complex-type N-glycans, which we used to define complete epitopes of two bNAbs. Env trimer was complexed with 10-1074 (against the V3-loop) and IOMA, a new CD4-binding site (CD4bs) antibody. Although IOMA derives from VH1-2*02, the germline gene of CD4bs-targeting VRC01-class bNAbs, its light chain lacks the short CDRL3 that defines VRC01-class bNAbs. Thus IOMA resembles 8ANC131-class/VH1-46–derived CD4bs bNAbs, which have normal-length CDRL3s. The existence of bNAbs that combine features of VRC01-class and 8ANC131-class antibodies has implications for immunization strategies targeting VRC01-like bNAbs.

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Acknowledgements

We thank L. Stamatatos, M. Crispin, and A.-J. Behrens for helpful discussions; J. Vielmetter, J. Nhan, and the Caltech Protein Expression Center for producing proteins; P. Gnanapragasam for performing in-house neutralization assays; J. Kaiser for assistance with data processing; K. Vellizon and N. Thomas for assistance with FACS sorting; T. Oliveira for bioinformatic analyses; M. Murphy and H. Wang for assistance in making figures; the beamline staff at SSRL; A. Hurley (Rockefeller University Hospital) and C. Lehmann and G. Kremer (Infectious Disease Division at the University Hospital Cologne) for supporting the collection of patient material; and members of the Bjorkman and Nussenzweig laboratories for critical reading of the manuscript. This research was supported by National Institute Of Allergy And Infectious Diseases of the National Institutes of Health grant HIVRAD P01 AI100148 (P.J.B.) (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health), the Bill and Melinda Gates Foundation (Collaboration for AIDS Vaccine Discovery Grant OPP1124068 (M.C.N. and P.J.B.)), Comprehensive Antibody-Vaccine Immune Monitoring Consortium grant 1032144 (M.S.S.), the Rockefeller University Center for Clinical and Translational Science grant UL1 TR000043/KL2TR000151 from the National Center for Advancing Translational Sciences (L.v.B.), and the Molecular Observatory at Caltech, supported by the Gordon and Betty Moore Foundation. F.K. is supported by the Heisenberg-Program of the DFG (KL 2389/2-1), the European Research Council (ERC-StG639961), and the German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany. Operations at the Stanford Synchrotron Radiation Lightsource are supported by the US Department of Energy and the National Institutes of Health.

Author information

Author notes

    • Harry B Gristick
    •  & Lotta von Boehmer

    These authors contributed equally to this work.

Affiliations

  1. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.

    • Harry B Gristick
    • , Anthony P West Jr
    • , Michael Schamber
    •  & Pamela J Bjorkman
  2. Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA.

    • Lotta von Boehmer
    • , Anna Gazumyan
    • , Jovana Golijanin
    •  & Michel C Nussenzweig
  3. Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.

    • Michael S Seaman
  4. Department of Internal Medicine I, University Hospital of Cologne, Cologne, Germany.

    • Gerd Fätkenheuer
  5. German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.

    • Gerd Fätkenheuer
    •  & Florian Klein
  6. Laboratory of Experimental Immunology, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.

    • Florian Klein
  7. Department of Internal Medicine I, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany.

    • Florian Klein
  8. Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA.

    • Michel C Nussenzweig

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Contributions

H.B.G., L.v.B., A.P.W. Jr., M.C.N., and P.J.B. conceived the experiments; H.B.G. solved and analyzed crystal structures; L.v.B. performed single-cell experiments and isolated, cloned, and analyzed R1 antibodies; A.P.W. Jr. performed computational and bioinformatics analyses of VRC01-class, IOMA-class, and 8ANC131-class antibodies; H.B.G. and M.S. purified proteins for crystallography and optimized crystals; A.G. and J.G. produced monoclonal antibodies; M.S.S. conducted in vitro neutralization assays; F.K. and G.F. were the principal investigators for the clinical protocols and provided serum and PBMCs of subject R1; H.B.G., L.v.B., A.P.W., M.C.N. and P.J.B. wrote the paper, on which all principal investigators commented.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Pamela J Bjorkman.

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https://doi.org/10.1038/nsmb.3291

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