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HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design

Dam, Kim-Marie A. and Barnes, Christopher O. and Gristick, Harry B. and Schoofs, Till and Nussenzweig, Michel C. and Bjorkman, Pamela J. (2022) HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design. . (Unpublished)

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BG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate with BG24 neutralization of HIV-1, we solved 4.1 Å and 3.4 Å single-particle cryo-EM structures of two inferred germline (iGL) BG24 precursors complexed with engineered Env-based immunogens lacking CD4bs N-glycans. Structures revealed critical Env contacts by BG24_(iGL) and identified antibody light chain structural features that impede Env recognition. In addition, biochemical data and cryo-EM structures of BG24_(iGL) variants bound to Envs with CD4bs glycans present provided insights into N-glycan accommodation, including structural modes of light chain adaptations in the presence of the N276_(gp120) glycan. Together, these findings revealed Env regions critical for germline antibody recognition and potential sites to alter in immunogen design.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper ItemJournal Article
Dam, Kim-Marie A.0000-0002-1416-4757
Barnes, Christopher O.0000-0003-2754-5951
Gristick, Harry B.0000-0002-1957-2821
Schoofs, Till0000-0002-3584-8736
Nussenzweig, Michel C.0000-0003-0592-8564
Bjorkman, Pamela J.0000-0002-2277-3990
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-NC-ND 4.0 International license. This version posted March 26, 2022. We thank J. Vielmetter, P. Hoffman, and the Protein Expression Center in the Beckman Institute at Caltech for expression assistance. Electron microscopy was performed in the Caltech Cryo-EM Center with assistance from S. Chen and A. Malyutin. We thank the Gordon and Betty Moore and Beckman Foundations for gifts to Caltech to support the Molecular Observatory (Dr. Jens Kaiser, Director) and the beamline staff at SSRL for data collection assistance. 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-c76SF00515. 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 (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. C.O.B. was supported by a Burroughs Wellcome PDEP fellowship and HHMI Hanna Gray Fellowship. This work was supported by the National Institute of Allergy and Infectious Diseases (NIAID) Grant HIVRAD P01 AI100148 (to P.J.B. and M.C.N.), the Bill and Melinda Gates Foundation Collaboration for AIDS Vaccine Discovery (CAVD) grant INV-002143 (P.J.B., M.C.N.), and NIH P50 AI150464 (P.J.B.). Author contributions: K.A.D., C.O.B., H.B.G., T.S., M.C.N., and P.J.B. designed the research. K.A.D. performed experiments and K.A.D., C.O.B., and H.B.G. analyzed results. K.A.D. and P.J.B. wrote the manuscript with input from co-authors. The authors declare that there are no competing interests. Data availability: The atomic model generated for the X-ray crystallography structure of the BG24_(iGL-CDR3mat) Fab in this study has been deposited in the Protein Data Bank (PDB) under accession code 7UGM. The cryo-EM maps and atomic structures have been deposited in the PDB and/or Electron Microscopy Data Bank (EMDB) under accession codes 7UGN and EMD-26490 for BG24_(iGL-CDR3iGL)-GT1-10-1074 Class 1, EMD-26491 for BG24_(iGL-CDR3iGL)-GT1-10-1074 Class 2, 7UGO and EMD-26492 for BG24_(iGL-CDR3mat)-GT1-10-1074, 7UGP and EMD-26493 forBG24_(iGL-LC)-GT1_(N276gp120)-10-1074 Class 1, EMD-26494 for BG24_(iGL-LC)-GT1_(N276gp120)-10-1074 Class 2, EMD-26495 for BG24_(iGL-LC)-GT1_(N276gp120)-10-1074 Class 3, and 7UGQ and EMD-26496 for BG24_(CDRL-iGL)-6405-10-1074. Local refinement maps used to model CDRL1s of BG24-derivatives have been deposited with PDB and EMDB accession codes for each respective structure.
Funding AgencyGrant Number
Gordon and Betty Moore FoundationUNSPECIFIED
Arnold and Mabel Beckman FoundationUNSPECIFIED
Department of Energy (DOE)DE-AC02-C76SF00515
Burroughs Wellcome FundUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Bill and Melinda Gates FoundationINV-002143
NIHP50 AI150464
Record Number:CaltechAUTHORS:20220328-189268500
Persistent URL:
Official Citation:HIV-1 CD4-binding site germline antibody–Env structures inform vaccine design. Kim-Marie A. Dam, Christopher O. Barnes, Harry B. Gristick, Till Schoofs, Michel C. Nussenzweig, Pamela J. Bjorkman. bioRxiv 2022.03.25.485873; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:114104
Deposited By: Tony Diaz
Deposited On:28 Mar 2022 21:21
Last Modified:18 Nov 2022 00:06

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