Cell Host & Microbe, Volume 19 Supplemental Information Structures of the Zika Virus Envelope Protein and Its Complex with a Flavivirus Broadly Protective Antibody Lianpan Dai, Jian Song, Xishan Lu, Yong-Qiang Deng, Abednego Moki Musyoki, Huijun Cheng, Yanfang Zhang, Yuan Yuan, Hao Song, Joel Haywood, Haixia Xiao, Jinghua Yan, Yi Shi, Cheng-Feng Qin, Jianxun Qi, and George F. Gao
Figure S1. Electrostatic surface view of ZIKV-E and other flavivirus E structures, related to Figure 1B. Comparison of an electrostatic surface potential map of ZIKV-E with other structure-known flavivirus E, including tick-borne encephalitis virus (TBEV) (PDB code: 1SVB), DENV2 (PDB code: 4UTC), DENV3 (PDB code: 1UZG), Japanese encephalitis virus (JEV) (PDB code: 3P54) and WNV (PDB code: 2HG0), revealed that a strong positive charge is found at the fusion loop region of E-dimer due to the presence of a conserved R99 residue at the protein surface. Notably, however, ZIKV displays a uniquely positively charged patch region adjacent to the fusion loop region in domain I due to the existence of R138, R164 and K166 unique to the ZIKV (also see the sequence alignment in Figure S2). The contour levels are around 60 +/- kt/e.
Figure S2. Sequence alignment of flavivius E protein and especially the residues in fusion loop and DENV EDE mab/e interaction regions, related to Figure 1 and Figure 6. The Sequence alignment of full-length E protein from DENV 1-4, ZIKV, WNV and YFV are depicted, with residues in dark red or light blue background highlighting identity and similarity, respectively. Coloured boxes highlight the fusion loop region and five distinct regions of E protein for DENV EDE mab binding.
Figure S3. Superimposition of ZIKV-E/2A10G6, WNV-E/E53 and DENV2-E/A11 complexes, related to Figure 6. For fusion loop epitope (FLE) antibodies, 2A10G6 binds to tip of domain II at a perpendicular angle, whereas E53 binds to the fusion loop region at tilted angle. For E-dimer dependent epitope (EDE) antibody, A11 binds to the top surface of E-dimer around the fusion loop region.
Figure S4. Structural models of 2A10G6 bound to envelope (E) protein of DENV2 and WNV, related to Figure 4. The DENV2-E (PDB code: 1OKE) and WNV-E (PDB code: 2HG0) structures are superimposed with the ZIKV-E structure, and the conformations of fusion loop are highly conserved among these flavivirus E structures. It indicates that 2A10G6 can bind to the DENV-E and WNV-E with a similar mode.
Table S1. Data collection and refinement statistics for ZIKV E and complex of ZIKA E-2A10G6 complex, related to Figure 1 and Figure 4. ZIKV E ZIKV E-2A10G6 Data collection Space group P 21 P 21 Cell dimensions a, b, c (Å) 76.45, 59.06, 49.60, 104.85, 81.86 103.67 ( ) 90.00, 103.72, 90.00, 102.70, 90.00 90.00 Resolution (Å) 50-2.00 (2.07-2.00) 50-3.00 (3.11-3.00) R merge 0.12 (0.62) 0.18 (1.17) R pim 0.05 (0.25) 0.09 (0.58) CC 1/2 (%) 0.994(0.86) 0.992(0.55) I / I 13.5 (1.9) 9.0 (1.2) Completeness (%) 93.3 (75.0) 98.6 (92.4) Number of unique reflections 57290 16275 Redundancy 7.0 (5.7) 4.6 (4.3) Refinement Resolution (Å) 33.98-2.00 30.69-3.00 No. reflections 57258 16253 R work / R free 0.20/0.23 0.23/0.27 No. atoms Protein 5971 6087 Ligand/ion 0 0 Water 328 0 B-factors Protein 38.0 79.0/67.7 Ligand/ion Water 37.1 R.m.s. deviations Bond lengths (Å) 0.005 0.005 Bond angles ( ) 0.985 0.928 Ramachandran plot(%) Most favored 89.1 77.0 Additionally favored 9.3 19.9 Generally allowed 1.6 3.1 Disallowed 0 0 Highest resolution shell statistics are shown in parentheses.
Table S2. Analysis of N67 and N153 glycosylation sites in the isolated ZIKV strains, related to Figure 6. N67 site N153 site Zika Strains 67 68 69 154* 155 156 CONSERVATION MR 777 D M A N D T - + 8375 D M A N D T - + 103344 D M A N D T - + ArB1362 D M A N D N - - ArB7701 D M A N D I - - ArB15076 D M A N D E - - ArD_41519 D M A N D T - + ArD7117 D M A N D I - - ArD128000 D M A G H E - - ArD157995 D M A N D I - - ArD158084 D M A N D I - + BeH815744 D M A N D T - + BeH818995 D M A N D T - + BeH819015 D M A N D T - + BeH819966 D M A N D T - + BeH823339 D I A N D T - + BeH828305 D M A N D T - + Brazil-ZKV2015 D M A N D T - + Dominican D M A N D T - + FB-GWUH-2016 D M A N D T - + FLR D M A N D T - + FSS13025 D M A N D I - - GD01 D M A N D T - + GDZ16001 D M A N D T - + GZ01 D M A N D T - + Haiti/1225/2014 D M A N D T - + H/PF/2013 D M A N D T - + IbH_30656 D M A N D E - - MEX/InDRE/Lm/2016 D M A N D T - + MEX/InDRE/Sm/2016 D M A N D T - + MRS_OPY/M_P/2015 D M A N D T - + Natal RGN D M A N D T - + P6-740 D M A N D G - - PHL/2012/CPC-0740 D M A N D T - + PRVABC59 D M A N D T - + Rio-S1 D M A N D T - + Rio-U1 D M A N D T - + SSABR1 D M A N D T - + SZ01/2016 D M A N D T - + THA/2014/SV0127-14 D M A N D T - + VE_Ganxian D M A N D T - +
Z1106033 D M A N D T - + ZikaSPH2015 D M A N D T - + ZJ03 D M A N D T - + *The 150-loop is variable in different flaviviruses, resulting from mutation, insertion and deletion. For ZIKV, the glycosylation site in 150-loop is N154, which is equivalent to the N153 glycosylation site in dengue viruses.