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Convergence of a common solution to broad ebolavirus neutralization by glycan cap directed human antibodies

Murin, Charles D. and Gilchuk, Pavlo and Ilinykh, Philipp A. and Huang, Kai and Kuzmina, Natalia and Shen, Xiaoli and Brunh, Jessica F. and Brunh, Aubrey L. and Davidson, Edgar and Doranz, Benjamin J. and Williamson, Lauren E. and Copps, Jeffrey and Alkutkar, Tanwee and Flyak, Andrew I. and Bukreyev, Alexander and Crowe, James E., Jr. and Ward, Andrew B. (2020) Convergence of a common solution to broad ebolavirus neutralization by glycan cap directed human antibodies. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20201015-152733216

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Abstract

Antibodies that target the glycan cap epitope on ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization is not well-understood. Here we present cryo-electron microscopy (cryo-EM) structures of several glycan cap antibodies that variably synergize with GP base-binding antibodies. These structures describe a conserved site of vulnerability that anchors the mucin-like domains (MLD) to the glycan cap, which we name the MLD-anchor and cradle. Antibodies that bind to the MLD-cradle share common features, including the use of IGHV1-69 and IGHJ6 germline genes, which exploit hydrophobic residues and form beta-hairpin structures to mimic the MLD-anchor, disrupt MLD attachment, destabilize GP quaternary structure and block cleavage events required for receptor binding. Our results collectively provide a molecular basis for ebolavirus neutralization by broadly reactive glycan cap antibodies.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.10.14.340026DOIDiscussion Paper
ORCID:
AuthorORCID
Murin, Charles D.0000-0002-1610-9276
Flyak, Andrew I.0000-0002-8722-479X
Bukreyev, Alexander0000-0002-0342-4824
Crowe, James E., Jr.0000-0002-0049-1079
Ward, Andrew B.0000-0001-7153-3769
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. This work was supported by NIH grants U19 AI109762 and U19 AI142785. T.A. is supported by a Kellogg Graduate Student Fellowship from Scripps Research. We would like to thank the Joint Center for Structural Genomics at Scripps Research and Henry Tien for assistance with setting up crystal trays. We like to thank Dr. Robyn Stanfield for assistance with looping and shipping crystals, for assistance with collecting X-ray diffraction data, reducing the data and phasing the crystal structure. We also thank Dr. Ian Wilson for generously sharing synchrotron time to collect X-ray diffraction data. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (including P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. The Jurkat-EBOV GP cell line was a kind gift form Carl Davis and Rafi Ahmed. We thank Hannah Turner, Bill Anderson, Jonathan Torres, Gabriel Ozorowski and Charles Bowman from Scripps Research for their assistance with cryo-EM sample prep, microscope operation, data collection and processing. Materials availability: Plasmids generated in this study are available upon request by the Lead Contact. Data and code availability: The cryo-EM maps and structural coordinates generated during this study are available at the Electron Microscopy Data Bank (www.ebi.ac.uk/pdbe/emdb) and the Worldwide Protein Data Bank (www.pdb.org). The accession codes for the following cryo-EM maps reported in this paper are: EMD-22839 (EBOV GPDMuc:BDBV289 Fab), EMD-22841 (BDBV GPDMuc:BDBV43 Fab and ADI-15878 Fab), EMD-22853 (EBOV GPDMuc:EBOV-437 Fab and EBOV-515 Fab), EMD-22848 (EBOV GPDMuc:EBOV-442 Fab and EBOV-515 Fab), EMD-22842 (EBOV GPDMuc:EBOV-293 Fab and EBOV-515 Fab), EMD-22847 (EBOV GPDMuc:EBOV-296 Fab and EBOV-515 Fab), EMD-22851 (EBOV GPDMuc:BDBV-329 Fab and EBOV-515 Fab) and EMD-22852 (EBOV GPDMuc:EBOV-237 Fab and EBOV-515 Fab). The accession codes for PDB files are: 7KEJ (EBOV GPDMuc:BDBV-289 Fab), 7KEW (BDBV GPDMuc:BDBV577 -43 Fab), 7KFH (EBOV GPDMuc:EBOV-437 Fab), 7KFB (EBOV GPDMuc:EBOV-442 Fab), 7KEX (EBOV GPDMuc:EBOV-293 Fab), 7KF9 (EBOV GPDMuc:EBOV-296 Fab), 7KFE (EBOV GPDMuc:BDBV-329 Fab) and 7KFG (unliganded BDBV289 Fab). Author contributions: C.D.M. performed protein production for all cryo-EM and kinetic experiments, performed cryo-EM experiments and analysis, crystallized the BDBV289 Fab and performed kinetic experiments and analysis. C.D.M. collected the crystal data and phased the data. J.F.B. built and validated the crystal structure. J.C. produced antibody Fab for the crystallography trials. P.G. performed synergy, cleavage assays and assembled information for Table 1. T.A. helped toperform GP stability assays and collect cryo-EM data. L.W. expressed and purified EBOV-237 and BDBV-329 Fab. P.A.I., K.H., N.K., X.S., A.I.F. and A.B. isolated and characterized EBOV-293 and EBOV-296. A.L.B., E.D. and B.J.D. performed alanine scanning and characterization of EBOV-293 and EBOV-296. C.D.M., P.G., A.B., J.E.C. and A.B.W. designed the experiments.C.D.M. wrote the manuscript. Competing Interest Statement: A.L.B., E.D., and B.J.D. are employees of Integral Molecular. B.J.D. is a shareholder of Integral Molecular. J.E.C. has served as a consultant for Sanofi and is on the Scientific Advisory Boards of CompuVax and Meissa Vaccines, is a recipient of previous unrelated research grants from Moderna and Sanofi and is founder of IDBiologics. Vanderbilt University has applied for a patent that is related to this work. All other authors declare no competing interests.
Funders:
Funding AgencyGrant Number
NIHU19 AI109762
NIHU19 AI142785
Scripps Research InstituteUNSPECIFIED
Department of Energy (DOE)DE-AC02-76SF00515
NIHP41GM103393
Subject Keywords:ebolaviruses, Ebola virus, antibody therapeutics, filoviruses, glycan cap, antibody, mAbs, broadly neutralizing
Record Number:CaltechAUTHORS:20201015-152733216
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20201015-152733216
Official Citation:Convergence of a common solution to broad ebolavirus neutralization by glycan cap directed human antibodies Charles D Murin, Pavlo Gilchuk, Philipp Ilinykh, Kai Huang, Natalia Kuzmina, Xiaoli Shen, Jessica F Brunh, Aubrey L Brunh, Edgar Davidson, Benjamin Doranz, Lauren E Williamson, Jeffrey Copps, Tanwee Alkutkar, Andrew I Flyak, Alexander Bukreyev, James E. Crowe, Andrew B Ward bioRxiv 2020.10.14.340026; doi: https://doi.org/10.1101/2020.10.14.340026
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106092
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:16 Oct 2020 16:42
Last Modified:16 Oct 2020 16:42

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