# Elucidating the Molecular Mechanism of 3D1 Antibody Binding to a Swine Enteric Coronavirus Antigen

## TL;DR

This study reveals how the 3D1 antibody neutralizes a swine coronavirus by binding to a specific viral protein structure, preventing the virus from fusing with host cells.

## Contribution

The study identifies a conserved epitope and mechanism by which 3D1 traps a pre-hairpin intermediate state of the viral spike protein.

## Key findings

- 3D1 binds to a linear β-turn motif in the HR1 domain of the viral spike protein with high affinity.
- 3D1 competitively inhibits the interaction between HR1 and HR2, blocking the formation of the postfusion six-helix bundle.
- 3D1 maintains strong binding to HR1 even when it is in a conformationally constrained, helical state.

## Abstract

The broadly neutralizing monoclonal antibody 3D1 potently neutralizes SADS-CoV by targeting a conserved epitope within the heptad repeat 1 (HR1) domain of the viral spike protein. Structural and biophysical analyses demonstrate that 3D1 binds with high affinity to a specific linear β-turn motif (residues A804–N809) in HR1. High-resolution crystallography reveals that this motif sits within a deep, electrostatically complementary paratope groove. Critically, 3D1 binding competitively inhibits the essential interaction between HR1 and HR2. Notably, its recognition is not dependent on HR1’s native helical conformation, as it maintains strong binding to conformationally constrained, stapled helical peptides. Collectively, the data indicate that 3D1 neutralizes by capturing a pre-hairpin intermediate state of HR1—a transition state between prefusion and postfusion forms—thereby sterically blocking the formation of the stable postfusion six-helix bundle that is essential for membrane fusion. This work defines a precise, structure-dependent neutralizing epitope and elucidates a mechanism of action that involves trapping a key fusion intermediate, offering a valuable template for the design of broad-spectrum coronavirus therapeutics.