Structural repertoire of HIV-1-neutralizing antibodies targeting the CD4 supersite in 14 donors

The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures –8 determined here– of CD4bs antibodies from 14 donors. The 16 antibodies segregated by recognition mode and developmental ontogeny into two types: CDR H3-dominated and VH-gene-restricted. Both could achieve greater than 80% neutralization breadth, and both could develop in the same donor. Although paratope chemistries differed, all 16 gp120-CD4bs antibody complexes showed geometric similarity, with antibody-neutralization breadth correlating with antibody-angle of approach relative to the most effective antibody of each type. The repertoire for effective recognition of the CD4 supersite thus comprises antibodies with distinct paratopes arrayed about two optimal geometric orientations, one achieved by CDR H3 ontogenies and the other achieved by VH-gene-restricted ontogenies. To whom correspondence should be addressed: [email protected] (J.R.M.) and [email protected] (P.D.K.). *Equal contribution. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. AUTHOR CONTRIBUTIONS T.Z., R.M.L, L.C., P.A., L.Sh., J.R.M. and P.D.K. designed research, analyzed data, and assembled and wrote the paper, on which all principal investigators commented. R.M.L., X.W. and N.A.D. isolated and characterized VRC13, VRC16, VRC18 and VRC27 antibodies with assistance from M.J.E., L.T., and Z.Y., and with R.T.B, M.K.L., K.M., S.O. and S.D.S. performing neutralization assays. T.Z., L.C. and P.A. led the structure determination and analysis with assistance from T.S.L, S.M., S.S. and A.Z, and with A.D., Y.Y. and B.Z. expressing HIV-1 gp120 cores and antibodies for crystallization and binding and T.Z. and M.P. performing trimer modeling. L.C., M.G.J., M.D.G. and L.St. produced germline antibodies and assessed binding to HIV-1 gp120. R.M.L. and X.W. prepared samples for 454 pyrosequencing; NISC and J.C.M performed next-generation sequencing; C.S., L.Sh. and P.D.K. carried out bioinformatics. N.S.L. contributed to repertoire analysis, and A.P.W. and P.J.B. contributed to ontogeny analysis. I.S.G. performed neutralization fingerprinting, and T.K. and I.S.G. defined the CD4 supersite by antibody potency. T.G., H.-P.P., A.-S.Y. and L.Sh. analyzed antibody paratope chemistry. D.L. and R.K. performed B cell activation experiments. R.M.L. analyzed donor sera potency and breadth with D.R.B., W.C.K., M.S.C., B.F.H., J.P.C., M.C., J.F.S. and M.C.N. contributing donor samples. D.C., A.L, Q.J.S. and R.A.W provided antibody HJ16; J.F.S. and M.C.N. provided antibodies 1B2530, 8ANC131 and 8ANC134. ACCESSION NUMBERS Coordinates and structure factors for the CD4-binding site antibodies in complex with HIV-1 gp120 have been deposited with the Protein Data Bank under accession codes: 4YDJ, 4YDK, 4YDL, 4YDI, 4RWY, 4RX4, 4YFL and 4YE4. Nucleotide sequences for heavy chain variable regions of antibodies 44-VRC13.01, 44-VRC13.02, C38-VRC16.01, C38-VRC16.02 and C38-VRC18.02 have been deposited under Genbank accession numbers KP860914 through KP860918. Next-generation sequencing data for donors 44, C38 (for VRC16.01), RU01 and RU08 have been deposited with the National Center for Biotechnology Information Short Reads Archives (SRA) under accession code SRP055520. SUPPLEMENTAL INFORMATION Supplemental Information includes Extended Experimental Procedures, seven figures, and seven tables and can be found with this article online at http://dx.doi.org/xxx. HHS Public Access Author manuscript Cell. Author manuscript; available in PMC 2016 June 04. Published in final edited form as: Cell. 2015 June 4; 161(6): 1280–1292. doi:10.1016/j.cell.2015.05.007. A uhor M anscript