PDBsum entry 2z8v

Immune system

PDB id: 2z8v

Contents

Protein chains

335 a.a. *

116 a.a. *

Waters ×477

* Residue conservation analysis

PDB id:

2z8v

Name:

Immune system

Title:

Structure of an ignar-ama1 complex

Structure:

Apical membrane antigen 1. Chain: a, b. Fragment: domain i, ii, unp residues 104-438. Engineered: yes. New antigen receptor variable domain. Chain: c, d. Engineered: yes. Mutation: yes

Source:

Plasmodium falciparum. Organism_taxid: 36329. Strain: 3d7. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Orectolobus maculatus. Spotted wobbegong. Organism_taxid: 168098. Expressed in: escherichia coli.

Resolution:

2.35Å R-factor: 0.210 R-free: 0.285

Authors:

V.A.Streltsov,K.A.Henderson,A.H.Batchelor,A.M.Coley,S.D.Nuttall

Key ref:

K.A.Henderson et al. (2007). Structure of an IgNAR-AMA1 complex: targeting a conserved hydrophobic cleft broadens malarial strain recognition. Structure, 15, 1452-1466. PubMed id: 17997971 DOI: 10.1016/j.str.2007.09.011

Date:

11-Sep-07 Release date: 27-Nov-07

Protein chains

Q7KQK5  (Q7KQK5_PLAF7) -  Apical membrane antigen 1 from Plasmodium falciparum (isolate 3D7)

Seq: 622 a.a.

Struc: 335 a.a.

Protein chains

Q6X1E6  (Q6X1E6_9CHON) -  New antigen receptor variable domain (Fragment) from Orectolobus maculatus

Seq: 113 a.a.

Struc: 116 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1016/j.str.2007.09.011

Structure 15:1452-1466 (2007)

PubMed id: 17997971

Structure of an IgNAR-AMA1 complex: targeting a conserved hydrophobic cleft broadens malarial strain recognition.

K.A.Henderson, V.A.Streltsov, A.M.Coley, O.Dolezal, P.J.Hudson, A.H.Batchelor, A.Gupta, T.Bai, V.J.Murphy, R.F.Anders, M.Foley, S.D.Nuttall.

ABSTRACT

Apical membrane antigen 1 (AMA1) is essential for invasion of erythrocytes and hepatocytes by Plasmodium parasites and is a leading malarial vaccine candidate. Although conventional antibodies to AMA1 can prevent such invasion, extensive polymorphisms within surface-exposed loops may limit the ability of these AMA1-induced antibodies to protect against all parasite genotypes. Using an AMA1-specific IgNAR single-variable-domain antibody, we performed targeted mutagenesis and selection against AMA1 from three P. falciparum strains. We present cocrystal structures of two antibody-AMA1 complexes which reveal extended IgNAR CDR3 loops penetrating deep into a hydrophobic cleft on the antigen surface and contacting residues conserved across parasite species. Comparison of a series of affinity-enhancing mutations allowed dissection of their relative contributions to binding kinetics and correlation with inhibition of erythrocyte invasion. These findings provide insights into mechanisms of single-domain antibody binding, and may enable design of reagents targeting otherwise cryptic epitopes in pathogen antigens.

Selected figure(s)

Figure 5.
Figure 5. V[NAR]-AMA1 Contacts
(A) Alignment of AMA1s from P. falciparum strains 3D7, W2mef, and HB3 (residues N104–E438). Residues polymorphic between strains are boxed. Conserved hydrophobic cleft residues are underlined and asterisked. Residues in contact with V[NAR]s 14I-1 and 14I1-M15 (magenta), 14I-1 only (red), or 14I1-M15 only (blue) are indicated.
(B) Stereo images of the 14I-1 backbone (red) penetrating the AMA1 hydrophobic cleft (gray). Side chains of AMA1 residues within 4 Å of the V[NAR] backbone are shown, including hydrophobic residues forming the base of the hydrophobic cleft (orange) and residues polymorphic between P. falciparum strains 3D7, W2mef, and HB3 (cyan).
(C) As for (B) except for 14I1-M15 backbone (blue).

Figure 6.
Figure 6. Mechanism of V[NAR] Binding
(A) V[NAR] residue Arg92 contacts AMA1 residues Asn173, Glu174, Pro185, Thr186, and Glu187 (<4 Å) in a series of hydrogen bond and salt bridge interactions in the 14I-1 crystallographic structure. Residue coloring is as for Figure 5.
(B) As for (A) except for the V[NAR] 14I1-M15 structure.
(C) V[NAR] residues Tyr94, Tyr96, and Leu98 in the 14I-1 structure contact hydrophobic cleft residues Phe183 and Tyr251, and associated residue Asn371, through a network of water-mediated hydrogen bonds and potential aromatic interactions.
(D) V[NAR] residues Leu89 and Phe100 in the 14I-1 structure are closely associated with AMA1 residues within the hydropobic cleft (Met190, Tyr202, Met224) and residues polymorphic between P. falciparum strains (Met190, Phe201).

The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 1452-1466) copyright 2007.

Figures were selected by an automated process.