PDBsum entry 2fx9

Immune system

PDB id: 2fx9

Contents

Protein chains

214 a.a. *

227 a.a. *

14 a.a. *

Waters ×403

* Residue conservation analysis

PDB id:

2fx9

Name:

Immune system

Title:

Crystal structure of HIV-1 neutralizing human fab 4e10 in complex with a thioether-linked peptide encompassing the 4e10 epitope on gp41

Structure:

Fab 4e10. Chain: l, m. Fragment: light chain. Engineered: yes. Fab 4e10. Chain: h, i. Fragment: heavy chain. Engineered: yes. Fragment of HIV glycoprotein gp41.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Synthetic: yes. Other_details: this sequence includes a fragment of the HIV envelope protein gp41

Resolution:

2.10Å R-factor: 0.236 R-free: 0.271

Authors:

R.M.F.Cardoso,F.M.Brunel,S.Ferguson,D.R.Burton,P.E.Dawson,I.A.Wilson

Key ref:

R.M.Cardoso et al. (2007). Structural basis of enhanced binding of extended and helically constrained peptide epitopes of the broadly neutralizing HIV-1 antibody 4E10. J Mol Biol, 365, 1533-1544. PubMed id: 17125793 DOI: 10.1016/j.jmb.2006.10.088

Date:

03-Feb-06 Release date: 19-Dec-06

Protein chains

No UniProt id for this chain

Struc: 214 a.a.

Protein chains

No UniProt id for this chain

Struc: 227 a.a.

Protein chains

P05880  (ENV_HV1W2) -  Envelope glycoprotein gp160 from Human immunodeficiency virus type 1 group M subtype B (isolate WMJ22)

Seq: 847 a.a.

Struc: 14 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1016/j.jmb.2006.10.088

J Mol Biol 365:1533-1544 (2007)

PubMed id: 17125793

Structural basis of enhanced binding of extended and helically constrained peptide epitopes of the broadly neutralizing HIV-1 antibody 4E10.

R.M.Cardoso, F.M.Brunel, S.Ferguson, M.Zwick, D.R.Burton, P.E.Dawson, I.A.Wilson.

ABSTRACT

Potent, broadly HIV-1 neutralizing antibodies (nAbs) may be invaluable for the design of an AIDS vaccine. 4E10 is the broadest HIV-1 nAb known to date and recognizes a contiguous and highly conserved helical epitope in the membrane-proximal region of gp41. The 4E10 epitope is thus an excellent target for vaccine design as it is also highly amenable to peptide engineering to enhance its helical character. To investigate the structural effect of both increasing the peptide length and of introducing helix-promoting constraints in the 4E10 epitope, we have determined crystal structures of Fab 4E10 bound to an optimized peptide epitope (NWFDITNWLWYIKKKK-NH(2)), an Aib-constrained peptide epitope (NWFDITNAibLWRR-NH(2)), and a thioether-linked peptide (NWFCITOWLWKKKK-NH(2)) to resolutions of 1.7 A, 2.1 A, and 2.2 A, respectively. The thioether-linked peptide is the first reported structure of a cyclic tethered helical peptide bound to an antibody. The introduced helix constraints limit the conformational flexibility of the peptides without affecting interactions with 4E10. The substantial increase in affinity (10 nM versus 10(4) nM of the IC(50) of the original KGND peptide template) is largely realized by 4E10 interaction with an additional helical turn at the peptide C terminus that includes Leu679 and Trp680. Thus, the core 4E10 epitope was extended and modified to a WFX(I/L)(T/S)XX(L/I)W motif, where X does not play a major role in 4E10 binding and can be used to introduce helical-promoting constraints in the peptide epitope.

Selected figure(s)

Figure 1.
Figure 1. Stereo view of the peptide structures in the 4E10 complex superimposed on the sigma A-weighted F[o]–F[c] electron density omit map contoured at 3.5σ (2.5σ for peptide 94-1). Clear electron density (cyan cage) is evident for peptide 104-2 (pink chain in (a)), peptide 94-1 (yellow chain in (b)), and peptide 33-1 (green chain in (c)) residues, except for K683-K686 at the C terminus of peptide 94-1. Figure 1. Stereo view of the peptide structures in the 4E10 complex superimposed on the sigma A-weighted F[o]–F[c] electron density omit map contoured at 3.5σ (2.5σ for peptide 94-1). Clear electron density (cyan cage) is evident for peptide 104-2 (pink chain in (a)), peptide 94-1 (yellow chain in (b)), and peptide 33-1 (green chain in (c)) residues, except for K683-K686 at the C terminus of peptide 94-1.

Figure 3.
Figure 3. Contacts between Fab 4E10 and its peptide epitope. Light, heavy, and peptide chains are shown in magenta (light pink side-chains), gray (green side-chain), and yellow (orange side-chains), respectively. Hydrogen bonds are shown as dotted lines. (a) Contacts between Fab 4E10 and key epitope residues Trp^P672, Phe^P673, and Thr^P676. The side-chains of Trp^P672 and Phe^P673 are involved in aromatic π-stacking interactions with 4E10 residues Tyr^L91, Trp^H47, and Phe^H100J. (b) Contacts between epitope residue Trp^P680 and CDR H3 of 4E10. Tyr^681 could help to stabilize Trp^P680 in an optimal conformation for interaction with the antibody. (c) The cluster of Ile/Leu residues at the combining site contributed by 4E10 CDR H2 residues and peptide residues Ile675, Leu679, and Ile682. Figure 3. Contacts between Fab 4E10 and its peptide epitope. Light, heavy, and peptide chains are shown in magenta (light pink side-chains), gray (green side-chain), and yellow (orange side-chains), respectively. Hydrogen bonds are shown as dotted lines. (a) Contacts between Fab 4E10 and key epitope residues Trp^P672, Phe^P673, and Thr^P676. The side-chains of Trp^P672 and Phe^P673 are involved in aromatic π-stacking interactions with 4E10 residues Tyr^L91, Trp^H47, and Phe^H100J. (b) Contacts between epitope residue Trp^P680 and CDR H3 of 4E10. Tyr^681 could help to stabilize Trp^P680 in an optimal conformation for interaction with the antibody. (c) The cluster of Ile/Leu residues at the combining site contributed by 4E10 CDR H2 residues and peptide residues Ile675, Leu679, and Ile682.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 365, 1533-1544) copyright 2007.

Figures were selected by an automated process.