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. 2016 Nov 24;7:13679.
doi: 10.1038/ncomms13679.

Neutralization Mechanism of a Highly Potent Antibody Against Zika Virus

Free PMC article

Neutralization Mechanism of a Highly Potent Antibody Against Zika Virus

Shuijun Zhang et al. Nat Commun. .
Free PMC article


The rapid spread of Zika virus (ZIKV), which causes microcephaly and Guillain-Barré syndrome, signals an urgency to identify therapeutics. Recent efforts to rescreen dengue virus human antibodies for ZIKV cross-neutralization activity showed antibody C10 as one of the most potent. To investigate the ability of the antibody to block fusion, we determined the cryoEM structures of the C10-ZIKV complex at pH levels mimicking the extracellular (pH8.0), early (pH6.5) and late endosomal (pH5.0) environments. The 4.0 Å resolution pH8.0 complex structure shows that the antibody binds to E proteins residues at the intra-dimer interface, and the virus quaternary structure-dependent inter-dimer and inter-raft interfaces. At pH6.5, antibody C10 locks all virus surface E proteins, and at pH5.0, it locks the E protein raft structure, suggesting that it prevents the structural rearrangement of the E proteins during the fusion event-a vital step for infection. This suggests antibody C10 could be a good therapeutic candidate.


Figure 1
Figure 1. CryoEM micrographs of the uncomplexed ZIKV control and the Fab C10-ZIKV complex samples at various pH levels.
The deformed particles and aggregates are indicated with red and black arrows, respectively. The right upper corner inset shows a quarter of a 2D class average of the round particles. The E protein layer is indicated with a green arrow, the outer and inner leaflets of the bilayer lipid membrane with cyan arrows. In the pH5.0 uncomplexed ZIKV control, the E protein layer is missing in the 2D class average. Bottom right inset in the pH5.0 uncomplexed ZIKV control is a median filtered (5 × 5 pixel) image that showed particles with hair-like protrusions (blue arrow), which are likely the E proteins flopping on the virus surface. Scale bar is 500 Å.
Figure 2
Figure 2. CryoEM maps of the Fab C10-ZIKV complex.
Structures at (a) pH8.0, (b) pH6.5, (c) pH5.0, determined to 4.0, 4.4 and 12 Å resolution, respectively. Left panels show the surface of the cryoEM maps. Densities corresponding to the E protein layer and Fabs are coloured in yellow and magenta, respectively. Black triangle indicates an asymmetric unit and the 5-, 3-, 2-fold vertices are labelled. Right panels show zoom-in views of the fitted molecules into the density maps. (a, right panel) The 4.0 Å resolution pH8.0 complex show well-resolved bulky side chain densities (grey mesh). The Cα backbone, the nitrogen and oxygen atoms are coloured in green, blue and red, respectively. (b, right panel) The 4.4 Å resolution pH6.5 complex map showed density (grey transparent surface) separation between the β strands. DII of E protein is coloured in yellow. (c, right panel) Densities of the 12 Å resolution pH5.0 complex showed clear borders and shapes corresponding to the Fab C10-E protein dimeric structures. The variable region of the Fab molecule, DI, DII and DIII of the E protein are coloured in green, red, yellow and blue, respectively.
Figure 3
Figure 3. The C10 epitopes on the pH8.0 ZIKV-C10 complex structure.
(a) The C10 epitopes (circled by green dots) in an E protein raft identified by using a distance cutoff of 5 Å between the side chains of Fab and the E protein. The Fab molecules bind to both ends of each E protein dimer. The DI, DII and DIII of the E proteins in one raft are coloured in red, yellow and blue, respectively, those in neighbouring rafts are in grey. The three individual E proteins in an asymmetric unit are labelled as A, B and C molecules and those in the neighbouring asymmetric unit within the raft as A′, B′ and C′. The epitope residues within the intra-dimer interface are shown as light blue spheres, those at the inter-dimer and inter-raft interfaces as red and dark blue spheres, respectively. (b) The epitope within the intra-dimer interface on B-B′ dimer. The ZIKV c10 epitope residues that are conserved (similar charges or hydrophobicity) and non-conserved when compared to DENV are shown as green and magenta spheres, respectively. (c) Charge complementarity of the C10 intra-dimer epitope with the Fab paratope. Positive, negative and neutral charges are coloured in blue, red and white, respectively. Possible interacting residues are labelled.
Figure 4
Figure 4. The radial movement of the E protein rafts in the ZIKV-C10 complex structure at pH5.0 compared to pH8.0.
(a) Comparison of a quarter of the cross-section of the pH8.0 and pH5.0 complex cryoEM maps. The pH8.0 complex cryoEM map is low-pass filtered to look similar to pH5.0 complex. The bilayer lipid membrane (green) of both maps is located at similar radii. The E protein layer (yellow) of the pH5.0 complex map, however, is at a larger radius. (b) Radial movement of A-C′ (top panel) and B-B′ (bottom panel) dimers in the pH5.0 complex structure compared to that at pH8.0. Side views of the dimers at pH5.0 (shades of red) and pH8.0 (shades of blue). The displacements of the ends of the dimer from pH8.0 to pH5.0 are indicated. Vertices are indicated. (c) The E protein inter-raft interactions of the pH5.0 complex structure are disrupted. One E protein raft of the pH8.0 and pH5.0 complex structures is coloured in blue and red, respectively, other surrounding rafts in grey. In the pH5.0 complex, the rafts are further apart from each other compared to the pH8.0 complex.

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