The 3.8 Å resolution cryo-EM structure of Zika virus

Abstract

The recent rapid spread of Zika virus and its unexpected linkage to birth defects and an autoimmune neurological syndrome have generated worldwide concern. Zika virus is a flavivirus like the dengue, yellow fever, and West Nile viruses. We present the 3.8 angstrom resolution structure of mature Zika virus, determined by cryo-electron microscopy (cryo-EM). The structure of Zika virus is similar to other known flavivirus structures, except for the ~10 amino acids that surround the Asn(154) glycosylation site in each of the 180 envelope glycoproteins that make up the icosahedral shell. The carbohydrate moiety associated with this residue, which is recognizable in the cryo-EM electron density, may function as an attachment site of the virus to host cells. This region varies not only among Zika virus strains but also in other flaviviruses, which suggests that differences in this region may influence virus transmission and disease.

Fig. 1. The cryo-EM structure of Zika virus at 3.8Å

A) A representative cryo-EM image of frozen, hydrated ZIKV showing the distribution of virion phenotypes. Smooth, mature virus particles are identified by a surrounding black box. A partially mature virus particle is identified by the yellow arrow. B) A surface-shaded depth cued representation of ZIKV viewed down the icosahedral two-fold axis. The asymmetric unit is identified by the black triangle. C) A cross-section of ZIKV showing the radial density distribution. Panels B and C are color-coded based on the following radii: up to 130Å, blue; 131Å to 150Å, cyan; 151Å to 190Å, green; 191Å to 230Å, yellow, from 231Å, red. The region shown in blue fails to follow icosahedral symmetry and therefore its density is uninterruptable as is the case with other flaviviruses. D) A plot of the Fourier shell coefficient (FSC). Based on the 0.143 criterion for the gold standard comparison of two independent data sets, the resolution of the reconstruction is 3.8Å. The x axis shows 1/resolution in Å⁻¹; the y axis shows the FSC value. E) The Cα backbone of the E and M proteins in the icosahedral ZIKV particle (same orientation as in Panel B above) showing the herringbone organization. The color code fits the standard designation of E protein domains I (red), domain II (yellow) and domain III (blue). F). Representative cryo-EM electron densities of several amino acids of the E protein.

Fig. 2. The structures of Zika virus E and M proteins

A) The E protein dimer is shown in ribbon form viewed down the two-fold axis. The color code fits the standard designation of E protein domains I (red), domain II (yellow) and domain III (blue). The underlying stem and transmembrane residues are shown (pink). The fusion loop (green; Fig. S1), Asn154 glycan, and the variable loop surrounding the Asn154 glycan (residues 145–160, cyan) are highlighted. B) Side view of the E-M dimer showing the three E ectodomains as well as the E stem/transmembrane domains (pink) and the M loop and stem/transmembrane domains (light blue). The E and M transmembrane domains are found within the lipid bilayer (Fig. 1C). All residues of M (1–75) and all but three residues of E (1–501) were identified in the density. The Asn154 glycan from one monomer is labeled and can be seen projecting from the surface.

Fig. 3. Comparison of E protein of Zika virus and other flaviviruses

A). The region of the E protein of ZIKV (H/PF/2013) along with other ZIKV strains is aligned to representative mosquito-transmitted flaviviruses. Approximately 40 residues of Domain 1 centered on the Asn154 glycosylation site are compared. The conserved glycosylation site at Asn153/154 is highlighted in blue. Red arrows represent secondary structures of ZIKV (sheets). The glycosylation motif N-X-S/T is underlined. The sequences for various flaviviruses were obtained from the Virus Pathogen Database and Analysis Resource (ViPR). Virus strains for which structural information was available were chosen where possible. GenBank Genome Accession codes for these viruses are as follows- ZIKV_Uganda_MR766(a): AY632535, ZIKV_Uganda_MR766(b): KU720415; ZIKV_FPolynesia_H/PF/2013: KJ776791; ZIKV_ Brazil_SPH2015: KU321639; DENV 1_SG/07K3640DK1/2008: GQ398255; DENV 2_16681: NC_001474; DENV 3_SG/05K863DK1/2005: EU081190; DENV4_SG/06K2270DK1/2005: GQ398256; WNV_Lineage1_Kunjin_MRM61C: D00246; WNV_Lineage2_NY99: DQ211652; JEV_SA14: D90194 and YFV_Asibi: AY640589. Sequence of the original isolate (ZIKV_MR766) varies based on the information source; it remains unclear whether this strain was glycosylated at N154 at the time of isolation or whether the glycosylation was acquired during passage through mouse brain. The sequences were manually aligned based on the structures of ZIKV and DENV2. B) Superposition of the Cα backbone of the ZIKV and DENV 2 E and M proteins. The DENV 2 proteins are shown in magenta while the ZIKV E protein is shown in cyan and the M protein in yellow. C) Electron density representing the glycan at Asn154. D) Superposition of the loop region surrounding the glycosylation site (ZIKV: 144 -166; DENV2: 144 -161) flanking the Asn154 glycan for ZIKV (cyan) and DENV2 (magenta).