A 2.8-Angstrom-Resolution Cryo-Electron Microscopy Structure of Human Parechovirus 3 in Complex with Fab from a Neutralizing Antibody

Abstract

Human parechovirus 3 (HPeV3) infection is associated with sepsis characterized by significant immune activation and subsequent tissue damage in neonates. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tools for early detection and the lack of a vaccine or specific antiviral therapy. Toward the latter, we present a 2.8-Å-resolution structure of HPeV3 in complex with fragments from a neutralizing human monoclonal antibody, AT12-015, using cryo-electron microscopy (cryo-EM) and image reconstruction. Modeling revealed that the epitope extends across neighboring asymmetric units with contributions from capsid proteins VP0, VP1, and VP3. Antibody decoration was found to block binding of HPeV3 to cultured cells. Additionally, at high resolution, it was possible to model a stretch of RNA inside the virion and, from this, identify the key features that drive and stabilize protein-RNA association during assembly. IMPORTANCE Human parechovirus 3 (HPeV3) is receiving increasing attention as a prevalent cause of sepsis-like symptoms in neonates, for which, despite the severity of disease, there are no effective treatments available. Structural and molecular insights into virus neutralization are urgently needed, especially as clinical cases are on the rise. Toward this goal, we present the first structure of HPeV3 in complex with fragments from a neutralizing monoclonal antibody. At high resolution, it was possible to precisely define the epitope that, when targeted, prevents virions from binding to cells. Such an atomic-level description is useful for understanding host-pathogen interactions and viral pathogenesis mechanisms and for finding potential cures for infection and disease.

Extracellular Albumin and Endosomal Ions Prime Enterovirus Particles for Uncoating That Can Be Prevented by Fatty Acid Saturation

“…5A) and their disordered termini (67). Trp 38 in VP2, a highly conserved residue in picornaviruses, points toward ordered RNA (61)(62)(63)(64)(65)(66). This interaction between the RNA and capsid is directly adjacent to the major fenestrations that appear in the treated capsid, where the RNA has moved radially outwards, maintaining this specific interaction (Fig.…”

“…The RNA-capsid interactions were resolved in structures of A-particles published for several enteroviruses, such as enterovirus 71, coxsackievirus A16, and rhinovirus 2, suggesting their importance in assisting RNA release (20,30,31). The genome is unique within the capsid; nevertheless, in some picornaviruses, the RNA is so well ordered that individual bases can be identified, ranging from one base to several (61)(62)(63)(64)(65)(66). Here, the icosahedral reconstructions also showed for the first time details of the RNA, though not resolved to the atomic level, inside the intact E1 particle and in the uncoating intermediate structure.…”

Genotypic diversity and dynamic nomenclature of Parechovirus A

“…about what phenotypes might be subject to selection. [63][64][65] Branch length estimates were reasonably congruent between models for shorter branches ( ≤0.05 expected substitutions per site) across all datasets (Figure 4). The long internal branches were systematically underestimated by the GTR model compared to estimates under aBSREL.…”

Cryo-EM Studies of Virus-Antibody Immune Complexes

“…Thus far, 3D reconstructions of virus-Fab complexes at atomic resolution are available for some picornaviruses, including rhinovirus B14 (RV-B14) (Dong et al 2017), human parechovirus 3 (HPeV3) (Domanska et al 2019), hepatovirus A (HAV) (Cao et al 2019) and enterovirus D68 (EV-D68) (Zheng et al 2019) (Table 1). The atomic models of the capsid protein were well-fitted in the cryo-EM density map for HPeV3 (Fig.…”