title: Crystal structure of the broadly cross-reactive HIV-1-neutralizing Fab X5 and fine mapping of its epitope.
abstract: The human monoclonal antibody Fab X5 neutralizes a broad range of HIV-1 primary isolates. The crystal structure of X5 has been determined at 1.9 A resolution. There are two crystallographically independent Fab fragments in the asymmetric unit. The crystallographic R value for the final model is 0.22. The antibody-combining site features a long (22 amino acid residues) CDR H3 with a protruding hook-shaped motif. The X5 structure and site-directed mutagenesis data suggest that X5 amino acid residues W100 and Y100F in the CDR H3 motif may be critical for the binding of Fab X5 to gp120. X5 bound to a complex of a CD4 mimetic and gp120 with approximately the same kinetics and affinity as to a CD4-gp120 complex, suggesting that specific interactions between CD4 and X5 are unlikely to contribute to the binding of X5 to gp120-CD4 complexes. Binding of X5 to alanine scanning mutants of gp120JR-CSF complexed with CD4 suggested a critical role of the highly conserved amino acid residues at positions 423 and 432. The X5 structure and fine mapping of its epitope may assist in the elucidation of the mechanisms of viral entry and neutralization, and the development of HIV-1 inhibitors and vaccines.
authors.affiliation: Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA.
authors.forename: Ramalakshmi
authors.initials: R
authors.lastname: Darbha
authors.forename: Sanjay
authors.initials: S
authors.lastname: Phogat
authors.forename: Aran F
authors.initials: AF
authors.lastname: Labrijn
authors.forename: Yuuei
authors.initials: Y
authors.lastname: Shu
authors.forename: Yijun
authors.initials: Y
authors.lastname: Gu
authors.forename: Michelle
authors.initials: M
authors.lastname: Andrykovitch
authors.forename: Mei-Yun
authors.initials: MY
authors.lastname: Zhang
authors.forename: Ralph
authors.initials: R
authors.lastname: Pantophlet
authors.forename: Loic
authors.initials: L
authors.lastname: Martin
authors.forename: Claudio
authors.initials: C
authors.lastname: Vita
authors.forename: Dennis R
authors.initials: DR
authors.lastname: Burton
authors.forename: Dimiter S
authors.initials: DS
authors.lastname: Dimitrov
authors.forename: Xinhua
authors.initials: X
authors.lastname: Ji
mesh_terms: D000911:Antibodies, Monoclonal / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000998:Antiviral Agents / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D015704:CD4 Antigens / Q000737:chemistry / Q000276:immunology / Q000378:metabolism; D003429:Cross Reactions / Q000235:genetics; D003460:Crystallization; D018360:Crystallography, X-Ray; D000939:Epitopes / Q000737:chemistry* / Q000276:immunology* / Q000378:metabolism; D015699:HIV Envelope Protein gp120 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015497:HIV-1 / Q000276:immunology* / Q000472:pathogenicity; D006801:Humans; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D009500:Neutralization Tests; D010449:Peptide Mapping / Q000379:methods; D017434:Protein Structure, Tertiary / Q000235:genetics; D020349:Surface Plasmon Resonance
chemical_list: D000911:Antibodies, Monoclonal; D000998:Antiviral Agents; D015704:CD4 Antigens; D000939:Epitopes; D015699:HIV Envelope Protein gp120; D007140:Immunoglobulin Fab Fragments