9DHW

Q23.MD39 in Complex with Fabs from antibodies CH01 iGL and 35O22

This is a non-PDB format compatible entry.

Summary for 9DHW

• Entry DOI: 10.2210/pdb9dhw/pdb
• EMDB information: 46884
• Descriptor: Q23.MD39 Surface protein gp120, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (16 entities in total)
• Functional Keywords: antibody, complex, viral protein, viral protein-immune system complex, viral protein/immune system
• Biological source: Human immunodeficiency virus 1; More
• Total number of polymer chains: 12
• Total formula weight: 356974.64

Authors

Lin, Z.J.,Cui, J.,Du, J.,Habib, R.,Kulp, D.,Pallesen, J. (deposition date: 2024-09-04, release date: 2025-12-17)

Primary citation

Habib, R.,Solieva, S.O.,Lin, Z.J.,Ghosh, S.,Bayruns, K.,Singh, M.,Agostino, C.J.,Tursi, N.J.,Sowers, K.J.,Huang, J.,Roark, R.S.,Purwar, M.,Park, Y.,Ayyanathan, K.,Li, H.,Carey, J.W.,Kim, A.,Park, J.,McCanna, M.E.,Skelly, A.N.,Chokkalingam, N.,Kriete, S.,Shupin, N.,Huynh, A.,Walker, S.,Sadeesh, R.,Laenger, N.,Du, J.,Cui, J.,Patel, A.,Escolano, A.,Kwong, P.D.,Shapiro, L.,Bowman, G.R.,Hahn, B.H.,Shaw, G.M.,Weiner, D.B.,Pallesen, J.,Kulp, D.W.
Deep Mining of the Human Antibody Repertoire Identifies Frequent and Genetically Diverse CDRH3 Topologies Targetable by Vaccination.
Biorxiv, 2025

PubMed Abstract: Germline targeting vaccination strategies against highly variable pathogens such as HIV aim to elicit broadly neutralizing antibodies (bnAbs) with particular immunogenetic or structural features. The V2 apex of the HIV Env protein is a promising target for a class of bnAbs that contain conserved structural motifs in the heavy chain complementarity determining region 3 (CDRH3). Here, we show that these structural motifs are targetable by vaccination by characterizing V2 apex 'axe-like' CDRH3s in the human repertoire and developing new immunogens capable of engaging them. We determined the frequency and diversity of axe-like CDHR3s in healthy human donors using a series of structural informatics approaches, finding these precursors in nearly 90% of donors. Axe-targeting immunogens based on the HIV Env Q23.17 bound axe-like precursors in cryo-EM structures, induced V2 apex-specific antibody responses in humanized mice, and induced axe-like heterologous neutralizing antibodies in rhesus macaques infected with a germline-targeted simian-human immunodeficiency virus. These results illustrate a new structure-guided immunoinformatic vaccine design paradigm that can be employed to elicit immunogenetically diverse yet structurally conserved classes of antibodies.

PubMed: 41332666
DOI: 10.1101/2024.10.04.616739

Experimental method

ELECTRON MICROSCOPY (3.35 Å)