title: Structure of an N276-Dependent HIV-1 Neutralizing Antibody Targeting a Rare V5 Glycan Hole Adjacent to the CD4 Binding Site.
abstract: All HIV-1-infected individuals develop strain-specific neutralizing antibodies to their infecting virus, which in some cases mature into broadly neutralizing antibodies. Defining the epitopes of strain-specific antibodies that overlap conserved sites of vulnerability might provide mechanistic insights into how broadly neutralizing antibodies arise. We previously described an HIV-1 clade C-infected donor, CAP257, who developed broadly neutralizing plasma antibodies targeting an N276 glycan-dependent epitope in the CD4 binding site. The initial CD4 binding site response potently neutralized the heterologous tier 2 clade B viral strain RHPA, which was used to design resurfaced gp120 antigens for single-B-cell sorting. Here we report the isolation and structural characterization of CAP257-RH1, an N276 glycan-dependent CD4 binding site antibody representative of the early CD4 binding site plasma response in donor CAP257. The cocrystal structure of CAP257-RH1 bound to RHPA gp120 revealed critical interactions with the N276 glycan, loop D, and V5, but not with aspartic acid 368, similarly to HJ16 and 179NC75. The CAP257-RH1 monoclonal antibody was derived from the immunoglobulin-variable IGHV3-33 and IGLV3-10 genes and neutralized RHPA but not the transmitted/founder virus from donor CAP257. Its narrow neutralization breadth was attributed to a binding angle that was incompatible with glycosylated V5 loops present in almost all HIV-1 strains, including the CAP257 transmitted/founder virus. Deep sequencing of autologous CAP257 viruses, however, revealed minority variants early in infection that lacked V5 glycans. These glycan-free V5 loops are unusual holes in the glycan shield that may have been necessary for initiating this N276 glycan-dependent CD4 binding site B-cell lineage.
  
  
  OBJECTIVE
  The conserved CD4 binding site on gp120 is a major target for HIV-1 vaccine design, but key events in the elicitation and maturation of different antibody lineages to this site remain elusive. Studies have shown that strain-specific antibodies can evolve into broadly neutralizing antibodies or in some cases act as helper lineages. Therefore, characterizing the epitopes of strain-specific antibodies may help to inform the design of HIV-1 immunogens to elicit broadly neutralizing antibodies. In this study, we isolate a narrowly neutralizing N276 glycan-dependent antibody and use X-ray crystallography and viral deep sequencing to describe how gp120 lacking glycans in V5 might have elicited these early glycan-dependent CD4 binding site antibodies. These data highlight how glycan holes can play a role in the elicitation of B-cell lineages targeting the CD4 binding site.
authors: Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.|Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.|Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
authors: Constantinos Kurt
authors: CK
authors: Wibmer
authors: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
authors: Jason
authors: J
authors: Gorman
authors: Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa.
authors: Colin S
authors: CS
authors: Anthony
authors: Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.|Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors: Nonhlanhla N
authors: NN
authors: Mkhize
authors: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
authors: Aliaksandr
authors: A
authors: Druz
authors: Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa.
authors: Talita
authors: T
authors: York
authors: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
authors: Stephen D
authors: SD
authors: Schmidt
authors: South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
authors: Phillip
authors: P
authors: Labuschagne
authors: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
authors: Mark K
authors: MK
authors: Louder
authors: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
authors: Robert T
authors: RT
authors: Bailer
authors: Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa.|Department of Epidemiology, Columbia University, New York, New York, USA.
authors: Salim S
authors: SS
authors: Abdool Karim
authors: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
authors: John R
authors: JR
authors: Mascola
authors: Institute of Infectious Disease and Molecular Medicine and Division of Medical Virology, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa.|Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa.
authors: Carolyn
authors: C
authors: Williamson
authors: Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.|Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.|Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa.
authors: Penny L
authors: PL
authors: Moore
authors: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA pdkwong@nih.gov lynnm@nicd.ac.za.
authors: Peter D
authors: PD
authors: Kwong
authors: Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa pdkwong@nih.gov lynnm@nicd.ac.za.|Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.|Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa.
authors: Lynn
authors: L
authors: Morris
mesh_terms: D016915:AIDS Vaccines / Q000276:immunology; D019138:Antibodies, Blocking / Q000276:immunology; D000911:Antibodies, Monoclonal / Q000276:immunology; D057134:Antibodies, Neutralizing / Q000276:immunology*; D001402:B-Lymphocytes / Q000276:immunology; D001666:Binding Sites, Antibody / Q000276:immunology*; D015704:CD4 Antigens / Q000276:immunology*; D002460:Cell Line; D018360:Crystallography, X-Ray / Q000379:methods; D000939:Epitopes / Q000276:immunology; D057809:HEK293 Cells; D015483:HIV Antibodies / Q000276:immunology; D015699:HIV Envelope Protein gp120 / Q000276:immunology; D015658:HIV Infections / Q000276:immunology; D015497:HIV-1; D006801:Humans; D011134:Polysaccharides / Q000276:immunology*
chemical_list: D016915:AIDS Vaccines; D019138:Antibodies, Blocking; D000911:Antibodies, Monoclonal; D057134:Antibodies, Neutralizing; D015704:CD4 Antigens; D000939:Epitopes; D015483:HIV Antibodies; D015699:HIV Envelope Protein gp120; D011134:Polysaccharides