Structures of Echovirus 30 in complex with its receptors inform a rational prediction for enterovirus receptor usage

Abstract

Receptor usage that determines cell tropism and drives viral classification closely correlates with the virus structure. Enterovirus B (EV-B) consists of several subgroups according to receptor usage, among which echovirus 30 (E30), a leading causative agent for human aseptic meningitis, utilizes FcRn as an uncoating receptor. However, receptors for many EVs remain unknown. Here we analyzed the atomic structures of E30 mature virion, empty-and A-particles, which reveals serotype-specific epitopes and striking conformational differences between the subgroups within EV-Bs. Of these, the VP1 BC loop markedly distinguishes E30 from other EV-Bs, indicative of a role as a structural marker for EV-B. By obtaining cryoelectron microscopy structures of E30 in complex with its receptor FcRn and CD55 and comparing its homologs, we deciphered the underlying molecular basis for receptor recognition. Together with experimentally derived viral receptor identifications, we developed a structure-based in silico algorithm to inform a rational prediction for EV receptor usage.

Serotype specific epitopes identified by neutralizing antibodies underpin immunogenic differences in Enterovirus B

“…To define the key epitopes and atomic determinants of the interactions between E30 and its two NAbs precisely, structural investigations of E30 in complex with Fab fragments from 6C5 and 4B10 were conducted. Cryo-EM micrographs of the formaldehydeinactivated E30 virions (see the coordinated submission by Wang et al 15 ) in complex with 6C5/4B10 Fab fragments were recorded using an FEI Titan Krios electron microscope equipped with a Gatan K2 Summit detector ( Supplementary Fig. 3).…”

“…The position of this binding site is similar to those observed previously for 11G1 antibody bound to Enterovirus D68 (EVD68) and NAb 1D5 bound to Coxsackeivirus A6 (CVA6) 34 . Five 6C5 Fab molecules attach to the north rim of the canyon that constructs the "star-shaped" protrusions surrounding the mesa [see coordinated submission by Wang et al 15 ]. When compared to the 6C5 Fabs, the Fabs of 4B10, contacting the south wall of the canyon, are comparatively more spread out ( Fig.…”

“…vertically in an in-canyon attachment mode, resembling the strategy used by the uncoating receptor FcRn for its association with E30 [see coordinated submission by Wang et al 15 ]. In contrast, the 6C5 Fab inclines backward by~50°crossing the canyon from close to a fivefold axis toward an adjacent threefold axis ( Fig.…”

“…In general, protective antibody diversity, such as 6C5 and 4B10 elicited by E30, is an important feature of the adaptive immune system, wherein the system protects hosts against viral infection by producing diverse protective antibodies. Since E30 elicits production of strong neutralizing antibodies like 6C5 and 4B10, it qualifies as a reasonable vaccine candidate [see coordinated submission by Wang et al 15 ].…”

“…It is well known that many picornaviruses utilize two types of receptors, attachment and uncoating, to initiate efficient cellular entry processes, including viral attachment, endocytosis, internalization, uncoating and genome release [see coordinated submission by Wang et al 15 ] 16,17 . These processes are generally accompanied by a cascade of structural rearrangements of viral capsid proteins initiated and mediated by receptor binding as well as specific microenvironments [see coordinated submission by Wang et al 15 ] 6,[18][19][20][21][22][23][24][25][26] . Neutralizing antibodies could possibly target different steps of viral infection, including blocking viral attachment to the cellular receptor, interfering with viral uncoating via over-stabilizing or destabilizing the virus and physically damaging and/or aggregating the virus 12,27,28 .…”