PDBsum entry 3dro

Immune system

PDB id: 3dro

Contents

Protein chains

213 a.a. *

216 a.a. *

Ligands

LEU-GLU-LEU-ASP-LYS-TRP-ALA

* Residue conservation analysis

PDB id:

3dro

Name:

Immune system

Title:

Crystal structure of the HIV-1 cross neutralizing antibody 2f5 in complex with gp41 peptide elleldkwaslwn grown in ammonium sulfate

Structure:

2f5 fab light chain. Chain: a. Engineered: yes. 2f5 fab heavy chain. Chain: b. Engineered: yes. Elleldkwaslwn gp41 peptide. Chain: p. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expression_system_cell_line: hybridoma cells. Synthetic: yes. Other_details: the peptide was chemically synthesized by fmoc chemistry. The sequence naturally occurs in human immunodeficiency virus.

Resolution:

3.90Å R-factor: 0.222 R-free: 0.263

Authors:

J.-P.Julien,S.Bryson,E.F.Pai

Key ref:

J.P.Julien et al. (2008). Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site. J Mol Biol, 384, 377-392. PubMed id: 18824005 DOI: 10.1016/j.jmb.2008.09.024

Date:

11-Jul-08 Release date: 29-Jul-08

Protein chain

No UniProt id for this chain

Struc: 213 a.a.

Protein chain

Q6PYX1  (Q6PYX1_HUMAN) -  Hepatitis B virus receptor binding protein (Fragment) from Homo sapiens

Seq: 348 a.a.

Struc: 216 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

DOI no: 10.1016/j.jmb.2008.09.024

J Mol Biol 384:377-392 (2008)

PubMed id: 18824005

Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site.

J.P.Julien, S.Bryson, J.L.Nieva, E.F.Pai.

ABSTRACT

2F5 is a monoclonal antibody with potent and broadly neutralizing activity against HIV-1. It targets the membrane-proximal external region (MPER) of the gp41 subunit of the envelope glycoprotein and interferes with the process of fusion between viral and host cell membranes. This study presents eight 2F5 F(ab)' crystal structures in complex with various gp41 peptide epitopes. These structures reveal several key features of this antibody-antigen interaction. (1) Whenever free of contacts caused by crystal artifacts, the extended complementarity-determining region H3 loop is mobile; this is true for ligand-free and epitope-bound forms. (2) The interaction between the antibody and the gp41 ELDKWA epitope core is absolutely critical, and there are also close and specific contacts with residues located N-terminal to the epitope core. (3) Residues located at the C-terminus of the gp41 ELDKWA core do not interact as tightly with the antibody. However, in the presence of a larger peptide containing the gp41 fusion peptide segment, these residues adopt a conformation consistent with the start of an alpha-helix. (4) At high sulfate concentrations, the electron density maps of 2F5 F(ab)'-peptide complexes contain a peak that may mark a binding site for phosphate groups of negatively charged lipid headgroups. The refined atomic-level details of 2F5 paratope-epitope interactions revealed here should contribute to a better understanding of the mechanism of 2F5-based virus neutralization, in general, and prove important for the design of potential vaccine candidates intended to elicit 2F5-like antibody production.

Selected figure(s)

Figure 4.
Fig. 4. Superposition of the gp41 peptide epitope conformations found in eight different crystal structures. Superposition was performed using Cα atoms of the entire F[ab]′ fragment, in addition to the epitope peptide. gp41 peptide residues are shown as stick models: PDB ID 2P8L (green), PDB ID 3D0V (cyan), PDB ID 2P8P (magenta), PDB ID 1TJH (yellow), PDB ID 2P8M (salmon), PDB ID 3DRO (light gray), PDB ID 3D0L (blue), and PDB ID 3DRQ (orange). The conformation of residues ^651LELDKWAS^668 when bound to 2F5 F[ab]′ is conserved in all structures, whereas the conformation of residues ^669LW^670 varies significantly in structures 2P8P, 1TJH, and 3D0L. The RMSDs for all atoms of these peptides are given in Table 2.

Figure 5.
Fig. 5. Model representation of the interaction between bnmAb 2F5 and HIV-1 gp41. This figure was generated by performing a positional overlap of the 2F5 F[ab]′–gp41 epitope peptide ^514GIGALFLGFLGAAGS^528KK-Ahx-^655KNEQELLELDKWASLWN^671 crystal structure (PDB ID 3D0L) with the gp41 MPER ^662ELDKWASLWNWFNITNWLWYIK^683 structure in a lipid environment obtained by NMR/EPR/surface plasmon resonance (represented in yellow; PDB ID 2PV6) and presented by Sun et al.^38 The 2F5 epitope is represented in green, and the 2F5 F[ab]′ fragment is depicted as a vacuum electrostatic model, with blue indicating positively charged regions and with red indicating negatively charged regions; white represents nonpolar regions of the molecule. The orientation of the bnmAb 2F5 relative to the viral membrane is chosen based on assigning the position of the sulfate ion (in the green circle) to overlap with the headgroups of the viral membrane, the electrostatic charges on the surface of the F[ab]′, and the overlap of the α-helical MPER structures of the two models. Then, the mobile CDR H3 extended loop points towards the membrane, where it is hypothesized to interact with components of the membrane bilayer or with other parts of gp41 residing in or near the membrane. As there is no information available about the exact conformation of HR1, HR2, and FP of gp41 when binding to bnmAb 2F5, these parts have not been included in the model. The inset box shows a magnification of the 2F5 F[ab]′ interaction with its gp41 epitope. It displays the key residues of the 2F5 paratope (mostly CDR residues) involved in mediating the interaction with its antigen.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 384, 377-392) copyright 2008.

Figures were selected by the author.

Author's comment

The 8 crystal structures reported in this paper extend the epitope on gp41 recognized by the broadly neutralizing anti-HIV-1 antibody 2F5 towards the C-terminus; the additional residues can adopt a helical turn. We also show that without crystal constraints the very long CDR3(H) loop is mobile.
Emil F. Pai