7T0R

Crystal structure of the anti-CD4 adnectin 6940_B01 as a complex with the extracellular domains of CD4 and ibalizumab fAb

Summary for 7T0R

• Entry DOI: 10.2210/pdb7t0r/pdb
• Related: 7T0O
• Descriptor: Ibalizumab Light Chain, Ibalizumab Heavy Chain, T-cell surface glycoprotein CD4, ... (6 entities in total)
• Functional Keywords: inhibitor, hiv gp140, cd4, adnectin, ibalizumab, hiv env, combinectin, antiviral protein
• Biological source: Mus musculus (mouse); More
• Total number of polymer chains: 8
• Total formula weight: 202565.76

Authors

Williams, S.P.,Concha, N.O.,Wensel, D.L.,Hong, X. (deposition date: 2021-11-30, release date: 2022-01-12, Last modification date: 2024-10-16)

Primary citation

Wensel, D.,Williams, S.,Dixon, D.P.,Ward, P.,McCormick, P.,Concha, N.,Stewart, E.,Hong, X.,Mazzucco, C.,Pal, S.,Ding, B.,Fellinger, C.,Krystal, M.
Novel Bent Conformation of CD4 Induced by HIV-1 Inhibitor Indirectly Prevents Productive Viral Attachment.
J.Mol.Biol., 434:167395-167395, 2021

PubMed Abstract: GSK3732394 is a multi-specific biologic inhibitor of HIV entry currently under clinical evaluation. A key component of this molecule is an adnectin (6940_B01) that binds to CD4 and inhibits downstream actions of gp160. Studies were performed to determine the binding site of the adnectin on CD4 and to understand the mechanism of inhibition. Using hydrogen-deuterium exchange with mass spectrometry (HDX), CD4 peptides showed differential rates of deuteration (either enhanced or slowed) in the presence of the adnectin that mapped predominantly to the interface of domains 2 and 3 (D2-D3). In addition, an X-ray crystal structure of an ibalizumab Fab/CD4(D1-D4)/adnectin complex revealed an extensive interface between the adnectin and residues on CD4 domains D2-D4 that stabilize a novel T-shaped CD4 conformation. A cryo-EM map of the gp140/CD4/GSK3732394 complex clearly shows the bent conformation for CD4 while bound to gp140. Mutagenic analyses on CD4 confirmed that amino acid F202 forms a key interaction with the adnectin. In addition, amino acid L151 was shown to be a critical indirect determinant of the specificity for binding to the human CD4 protein over related primate CD4 molecules, as it appears to modulate CD4's flexibility to adopt the adnectin-bound conformation. The significant conformational change of CD4 upon adnectin binding brings the D1 domain of CD4 in proximity to the host cell membrane surface, thereby re-orienting the gp120 binding site in a direction that is inaccessible to incoming virus due to a steric clash between gp160 trimers on the virus surface and the target cell membrane.

PubMed: 34896364
DOI: 10.1016/j.jmb.2021.167395

Experimental method

X-RAY DIFFRACTION (3.65 Å)