3DRT

Crystal structure of the HIV-1 broadly neutralizing antibody 2F5 in complex with the gp41 scrambledFP-MPER scrHyb3K construct GIGAFGLLGFLAAGSKK-Ahx-K656NEQELLELDKWASLWN671

Summary for 3DRT

• Entry DOI: 10.2210/pdb3drt/pdb
• Related: 2P8M 3D0L 3DRO 3DRQ 3DRV
• Descriptor: 2F5 Fab' light chain, 2F5 Fab' heavy chain, scrHyb3K construct, ... (4 entities in total)
• Functional Keywords: hiv-1, gp41, 2f5, nmab, immune system
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 52263.78

Authors

Julien, J.-P.,Bryson, S.,de la Torre, B.G.,Andreu, D.,Nieva, J.L.,Pai, E.F. (deposition date: 2008-07-11, release date: 2009-06-23, Last modification date: 2024-10-30)

Primary citation

de la Arada, I.,Julien, J.P.,de la Torre, B.G.,Huarte, N.,Andreu, D.,Pai, E.F.,Arrondo, J.L.,Nieva, J.L.
Structural constraints imposed by the conserved fusion peptide on the HIV-1 gp41 epitope recognized by the broadly neutralizing antibody 2F5.
J.Phys.Chem.B, 113:13626-13637, 2009

PubMed Abstract: The HIV-1 gp41 epitope recognized by the broadly neutralizing 2F5 antibody has focused much attention as a suitable target in the design of peptide immunogens. Peptides mimicking the linear 2F5 epitope (2F5ep) are however intrinsically disordered, while the structural constraints existing in the cognate gp41 native structure recognized by the antibody are presently unknown. In recent reports, we have shown that core residues of the amino-terminal fusion peptide (FP) increase MAb2F5 affinity. Here, we have inferred the sequence-specific structural constraints imposed by the FP residues on the 2F5 epitope from the comparison of two hybrid peptides: HybK3, which connects through a flexible tether residues derived from 2F5ep and FP sequences, and scrHybK3, combining 2F5ep and an FP sequence with the conserved core scrambled. Circular dichroism, conventional and two-dimensional correlation infrared spectroscopy, and X-ray diffraction studies revealed specific structural features that were dependent on the exact FP sequence, namely, (i) the production with moderate low polarity of an intermediate folded structure enriched in beta-turns and alpha-helix; (ii) the existence in this intermediate of a thermotropic conformational transition taking place at ca. 18-20 degrees C, consistent with the conversion of 3(10)-helices into beta-turn conformers; and (iii) the presence of a C-terminal alpha-helix in crystals of Fab'-peptide complexes. Those features support the existence of native-like tertiary interactions between FP and 2F5 epitope residues, which might be important to recreate when developing an effective AIDS peptide vaccine.

PubMed: 19754136
DOI: 10.1021/jp905965h

Experimental method

X-RAY DIFFRACTION (3.3 Å)