PDBsum entry 2dd8

Immune system/viral protein

PDB id: 2dd8

Contents

Protein chains

220 a.a.

212 a.a.

192 a.a.

Ligands

PO4

NAG

Waters ×298

References listed in PDB file

Key reference

Title

Structure of severe acute respiratory syndrome coronavirus receptor-Binding domain complexed with neutralizing antibody.

Authors

P.Prabakaran, J.Gan, Y.Feng, Z.Zhu, V.Choudhry, X.Xiao, X.Ji, D.S.Dimitrov.

Ref.

J Biol Chem, 2006, 281, 15829-15836. [DOI no: 10.1074/jbc.M600697200]

PubMed id

16597622

Abstract

The severe acute respiratory syndrome coronavirus (SARS-CoV, or SCV), which caused a world-wide epidemic in 2002 and 2003, binds to a receptor, angiotensin-converting enzyme 2 (ACE2), through the receptor-binding domain (RBD) of its envelope (spike, S) glycoprotein. The RBD is very immunogenic; it is a major SCV neutralization determinant and can elicit potent neutralizing antibodies capable of out-competing ACE2. However, the structural basis of RBD immunogenicity, RBD-mediated neutralization, and the role of RBD in entry steps following its binding to ACE2 have not been elucidated. By mimicking immune responses with the use of RBD as an antigen to screen a large human antibody library derived from healthy volunteers, we identified a novel potent cross-reactive SCV-neutralizing monoclonal antibody, m396, which competes with ACE2 for binding to RBD, and determined the crystal structure of the RBD-antibody complex at 2.3-A resolution. The antibody-bound RBD structure is completely defined, revealing two previously unresolved segments (residues 376-381 and 503-512) and a new disulfide bond (between residues 378 and 511). Interestingly, the overall structure of the m396-bound RBD is not significantly different from that of the ACE2-bound RBD. The antibody epitope is dominated by a 10-residue-long protruding beta6-beta7 loop with two putative ACE2-binding hotspot residues (Ile-489 and Tyr-491). These results provide a structural rationale for the function of a major determinant of SCV immunogenicity and neutralization, the development of SCV therapeutics based on the antibody paratope and epitope, and a retrovaccinology approach for the design of anti-SCV vaccines. The available structural information indicates that the SCV entry may not be mediated by ACE2-induced conformational changes in the RBD but may involve other conformational changes or/and yet to be identified coreceptors.

Figure 1.
FIGURE 1. Overall structure of the SCV RBD in complex with the neutralizing antibody Fab m396. The SCV RBD is in green, and the prominent neutralizing site comprising residues 482 through 491 ( 6– 7 loop) is in red. The side chains of two important residues, Ile-489 and Tyr-491, of the loop are shown as sticks. A portion of the structure shown in brown constitutes the 16 amino acid residues that were not observed in the RBD·ACE2 structure (20). The light and heavy chains of the Fab are shown in cyan and yellow, respectively, with labeled CDRs, H1, H2, H3, and L3, which make contacts with the RBD.

Figure 3.
FIGURE 3. Critical interactions between SCV RBD (green) and Fab m396 (yellow and cyan for heavy- and light-chain CDRs, respectively) depicted with 2F[o] – F[c] electron density maps contoured at the 1.0 level. CDRs H1, H2, and H3 recognize the major neutralizing site, the 6– 7 loop. L3 exclusively contacts minor binding sites with the involvement of bridging water molecules. a, H1 residues Ser-31 and Thr-33 form hydrogen bonds with RBD residues Thr-486 and Thr-488 via backbone-side chain interactions. b, H2 displays a concave surface and contributes to the specific interactions between H2 residues Thr-52 and Asn-58, and RBD residue Tyr-491. c, H3 residue Val-97 contacts the RBD and buries the largest surface area per residue (108 Å^2) among all residues of the antibody combining site. The carbonyl of Val-97 forms a hydrogen bond to the side-chain amide of Gln-492 of RBD. d, L3 is the only light chain CDR that binds to the RBD with two bridging water molecules (pink spheres) involved.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 15829-15836) copyright 2006.