5CIL

Crystal Structure of non-neutralizing version of 4E10 (WDWD) with epitope bound

Summary for 5CIL

• Entry DOI: 10.2210/pdb5cil/pdb
• Related: 5CIN 5CIP
• Descriptor: FAB 4E10 HEAVY CHAIN, FAB 4E10 LIGHT CHAIN, Peptide from the MPER region of the ENV protein of HIV-1, ... (7 entities in total)
• Functional Keywords: broadly neutralizing antibody, recombinant fab, env-peptide, hiv-1, epitope, immune system
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 49198.73

Authors

Caaveiro, J.M.M.,Rujas, E.,Nieva, J.L.,Tsumoto, K. (deposition date: 2015-07-13, release date: 2015-09-23, Last modification date: 2024-10-16)

Primary citation

Rujas, E.,Gulzar, N.,Morante, K.,Tsumoto, K.,Scott, J.K.,Nieva, J.L.,Caaveiro, J.M.M.
Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10
J.Virol., 89:11975-11989, 2015

PubMed Abstract: The 4E10 antibody recognizes the membrane-proximal external region (MPER) of the HIV-1 Env glycoprotein gp41 transmembrane subunit, exhibiting one of the broadest neutralizing activities known to date. The neutralizing activity of 4E10 requires solvent-exposed hydrophobic residues at the apex of the complementarity-determining region (CDR) H3 loop, but the molecular basis for this requirement has not been clarified. Here, we report the cocrystal structures and the energetic parameters of binding of a peptide bearing the 4E10-epitope sequence (4E10ep) to nonneutralizing versions of the 4E10 Fab. Nonneutralizing Fabs were obtained by shortening and decreasing the hydrophobicity of the CDR-H3 loop (termed ΔLoop) or by substituting the two tryptophan residues of the CDR-H3 apex with Asp residues (termed WDWD), which also decreases hydrophobicity but preserves the length of the loop. The analysis was complemented by the first crystal structure of the 4E10 Fab in its ligand-free state. Collectively, the data ruled out major conformational changes of CDR-H3 at any stage during the binding process (equilibrium or transition state). Although these mutations did not impact the affinity of wild-type Fab for the 4E10ep in solution, the two nonneutralizing versions of 4E10 were deficient in binding to MPER inserted in the plasma membrane (mimicking the environment faced by the antibody in vivo). The conclusions of our structure-function analysis strengthen the idea that to exert effective neutralization, the hydrophobic apex of the solvent-exposed CDR-H3 loop must recognize an antigenic structure more complex than just the linear α-helical epitope and likely constrained by the viral membrane lipids.

PubMed: 26378169
DOI: 10.1128/JVI.01793-15

Experimental method

X-RAY DIFFRACTION (1.81 Å)