3IDY

Crystal structure of HIV-gp120 core in complex with CD4-binding site antibody b13, space group C2221

Summary for 3IDY

• Entry DOI: 10.2210/pdb3idy/pdb
• Related: 3IDX
• Descriptor: HIV-1 HxBc2 gp120 core, Fab b13 heavy chain, Fab b13 light chain, ... (6 entities in total)
• Functional Keywords: hiv-1, antibody, gp120, b13, envelope glycan protein, cd4-binding site, aids, apoptosis, cell membrane, cleavage on pair of basic residues, disulfide bond, envelope protein, fusion protein, host-virus interaction, membrane, transmembrane, viral immunoevasion, virion, immune system
• Biological source: Human immunodeficiency virus 1; More
• Total number of polymer chains: 6
• Total formula weight: 173443.74

Authors

Chen, L.,Kwon, Y.D.,Zhou, T.,Wu, X.,O'Dell, S.,Cavacini, L.,Hessell, A.J.,Pancera, M.,Tang, M.,Xu, L.,Yang, Z.Y.,Zhang, M.Y.,Arthos, J.,Burton, D.R.,Dimitrov, D.S.,Nabel, G.J.,Posner, M.,Sodroski, J.,Wyatt, R.,Mascola, J.R.,Kwong, P.D. (deposition date: 2009-07-22, release date: 2009-11-17, Last modification date: 2024-11-20)

Primary citation

Chen, L.,Do Kwon, Y.,Zhou, T.,Wu, X.,O'Dell, S.,Cavacini, L.,Hessell, A.J.,Pancera, M.,Tang, M.,Xu, L.,Yang, Z.Y.,Zhang, M.Y.,Arthos, J.,Burton, D.R.,Dimitrov, D.S.,Nabel, G.J.,Posner, M.R.,Sodroski, J.,Wyatt, R.,Mascola, J.R.,Kwong, P.D.
Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120.
Science, 326:1123-1127, 2009

PubMed Abstract: The site on HIV-1 gp120 that binds to the CD4 receptor is vulnerable to antibodies. However, most antibodies that interact with this site cannot neutralize HIV-1. To understand the basis of this resistance, we determined co-crystal structures for two poorly neutralizing, CD4-binding site (CD4BS) antibodies, F105 and b13, in complexes with gp120. Both antibodies exhibited approach angles to gp120 similar to those of CD4 and a rare, broadly neutralizing CD4BS antibody, b12. Slight differences in recognition, however, resulted in substantial differences in F105- and b13-bound conformations relative to b12-bound gp120. Modeling and binding experiments revealed these conformations to be poorly compatible with the viral spike. This incompatibility, the consequence of slight differences in CD4BS recognition, renders HIV-1 resistant to all but the most accurately targeted antibodies.

PubMed: 19965434
DOI: 10.1126/science.1175868

Experimental method

X-RAY DIFFRACTION (3.2 Å)