Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of Coxsackie Virus A10

Abstract

Coxsackievirus A10 (CV-A10) is responsible for an escalating number of severe infections in children, but no prophylactics or therapeutics are currently available. KREMEN1 (KRM1) is the entry receptor for the largest receptor-group of hand-foot-and-mouth disease causing viruses, which includes CV-A10. We report here structures of CV-A10 mature virus alone and in complex with KRM1 as well as of the CV-A10 A-particle. The receptor spans the viral canyon with a large footprint on the virus surface. The footprint has some overlap with that seen for the neonatal Fc receptor complexed with enterovirus E6 but is larger and distinct from that of another enterovirus receptor SCARB2. Reduced occupancy of a particle-stabilising pocket factor in the complexed virus and the presence of both unbound and expanded virus particles suggests receptor binding initiates a cascade of conformational changes that produces expanded particles primed for viral uncoating.

Fig. 1. Overview structures of CV-A10 and its receptor complex.

Radially coloured surface representations of mature CV-A10 virus (a), CV-A10/KRM1 complex (b) and expanded CV-A10 A-particle (c). The first ordered residue of the VP1 N-terminus is coloured in magenta showing where it externalizes in c. Electron potential maps at icosahedral twofold axis of the mature CV-A10 (d), CV-A10/KRM1 complex (e) and CV-A10 A-particle (f). CV-A10/KRM1 interacting across the canyon from above (g) where a virus pentamer is drawn as a grey surface with one icosahedral pentameric subunit coloured with VP1 blue, VP2 green and VP3 red. KRM1 is drawn as a cartoon with the domains colour coded: KR magenta, WSC orange, CUB grey, adjacent receptors are colour coded in grey. Interaction of one virus protomer with KRM1 from the side closest to the KR domain (h), virus and receptor drawn as a cartoon keeping the same colours as in g. Interaction of one virus protomer with KRM1 from the side closest to the WSC domain (i), drawn as for h.

Fig. 2. Stereo diagram showing regions of KRM1 involved in interactions with DKK1 are used in engagement with CV-A10.

a Engagement between KRM1 and DKK1. b Engagement of KRM1 to CV-A10. DKK1 and CV-A10 are shown as surface representations with DKK1 in cyan and CV-A10 capsid proteins VP1, VP2 and VP3 in blue, green and red, respectively. KRM1 is drawn as ribbons with KR, WSC and CUB domains coloured in purple, orange and grey, respectively.

Fig. 3. The nature of the interactions between CV-A10 and KRM1 shown as open-book views.

CV-A10 (a) and KRM1 (b) interface. Both virus and receptor are shown as surface representations. VP1, VP2 and VP3 of CV-A10 are coloured in pale blue, green and red, respectively and an icosahedral subunit outlined with the fivefold (pentamer) and threefold (triangle) symmetry axes labelled, KRM1 from neighbouring subunits are shown in grey with domain names labelled in b. Contact areas between the virus and the receptor with distances ≤4.0 Å are shown in bright red, >4.0 Å and ≤9.0 Å in yellow. The contact areas attributable to two receptors bound at adjacent sites are shown in a. c, d Showing the contact areas on CV-A10 (c) and KRM1 (d) as electrostatic surfaces contoured at ±5 kT e⁻¹ (blue, positive; red, negative) with key residues from the interacting partner shown as sticks with main-chain backbones in orange and sidechains grey in c; residues involved in contacts from the virus capsid VP1, VP2 and VP3 are shown as blue, green and red sticks, respectively in d. e, f Open-book view of electrostatic surfaces of interactions between KRM1 (f) and DKK1 (e). Residues that contact CV-A10 (sticks in e) are also involved in interactions with DKK1 in the KRM1-DKK1-LPR6 complex. DKK1 is shown as ribbons in f.

Fig. 4. Details of interactions between CV-A10 and KRM1.

a KRM1 (orange ribbons) engaged in the canyon around the icosahedral fivefold axis of CV-A10. Only a pentamer of the virus is shown with VP1, VP2 and VP3 as pale blue, green and red surfaces, respectively. b–e Interactions of KRM1 with VP1 C-terminus (b), VP1 GH loop (c), VP2 EF loop (d) and VP3 GH loop (e) of the virus. The main-chain backbone and sidechains of KRM1 are drawn as orange sticks, and those for CV-A10 as blue, green and red sticks for VP1, VP2 and VP3, respectively.

Fig. 5. Comparison of amino acids in the receptor attachment area of CV-A10 strains and with other enteroviruses that cause HFMD.

a Residues in 14 strains of CV-A10 are highly conserved (33 out of 37) and 6 of the 31 residues are conserved among the KRM1-dependent type A enteroviruses, these are K140 and P141 in VP2 EF loop, G181, G182 and D185 in the VP3 GH loop, and Q240 at the C-terminus of VP3. Only one residue VP3 Q240 is conserved among 19 HFDV causing enteroviruses. KRM1 is shown as an electrostatic surface, residues of CV-A10 involved in contacts are shown as sticks with the same colour scheme as Fig. 3d, except the non-conserved sidechains are in grey. b Roadmap depiction of the virus surface (see “Methods” section). An icosahedral subunit is outlined in black lines and residues from VP1 are shown in blue, VP2 green and VP3 red with those in contact with KRM1 highlighted in the corresponding protein colour. Residues in contact with KRM1 and around the icosahedral symmetry axis are labelled.