Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 272.91 kDa 
• Atom Count: 15537 
• Modelled Residue Count: 2044 
• Deposited Residue Count: 2524 
• Unique protein chains: 3

5GZN

Structure of neutralizing antibody bound to Zika envelope protein

• PDB DOI: 10.2210/pdb5GZN/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Zika virus, Homo sapiens
• Expression System: Escherichia coli, Mammalian expression vector pBGSA
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2016-09-29 Released: 2016-12-28 
• Deposition Author(s): Wang, Q., Yang, H., Liu, X., Dai, L., Ma, T., Qi, J., Wong, G., Peng, R., Liu, S., Li, J., Li, S., Song, J., Liu, J., He, J., Yuan, H., Xiong, Y., Liao, Y., Li, J., Yang, J., Tong, Z., Griffin, B., Bi, Y., Liang, M., Xu, X., Cheng, G., Wang, P., Qiu, X., Kobinger, G., Shi, Y., Yan, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

Literature

Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus

Wang, Q., Yang, H., Liu, X., Dai, L., Ma, T., Qi, J., Wong, G., Peng, R., Liu, S., Li, J., Li, S., Song, J., Liu, J., He, J., Yuan, H., Xiong, Y., Liao, Y., Li, J., Yang, J., Tong, Z., Griffin, B.D., Bi, Y., Liang, M., Xu, X., Qin, C., Cheng, G., Zhang, X., Wang, P., Qiu, X., Kobinger, G., Shi, Y., Yan, J., Gao, G.F.

(2016) Sci Transl Med 8: 369ra179-369ra179

• PubMed: 27974667 
• DOI: 10.1126/scitranslmed.aai8336
• Primary Citation of Related Structures:  
  5GZN, 5GZO, 5GZR


• PubMed Abstract: 
  

The 2015-2016 outbreak of Zika virus (ZIKV) disease has affected many countries and is a major public health concern. ZIKV is associated with fetal microcephaly and neurological complications, and countermeasures are needed to treat and prevent ZIKV infection. We report the isolation of 13 specific human monoclonal antibodies from a single patient infected with ZIKV. Two of the isolated antibodies (Z23 and Z3L1) demonstrated potent ZIKV-specific neutralization in vitro without binding or neutralizing activity against strains 1 to 4 of dengue virus, the closest relative to ZIKV. These two antibodies provided postexposure protection to mice in vivo. Structural studies revealed that Z23 and Z3L1 bound to tertiary epitopes in envelope protein domain I, II, or III, indicating potential targets for ZIKV-specific therapy. Our results suggest the potential of antibody-based therapeutics and provide a structure-based rationale for the design of future ZIKV-specific vaccines.

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Organizational Affiliation: 

Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, D [auth B], G [auth E], H [auth G]	409	Zika virus	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for A0A1B0XTC8 (Zika virus) Explore A0A1B0XTC8  Go to UniProtKB:  A0A1B0XTC8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Heavy chain	E [auth C], B [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody light chain	F [auth D], C [auth L]	216	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.708	α = 90
b = 129.385	β = 90
c = 428.711	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-29 
• Released Date: 2016-12-28 
Deposition Author(s): Wang, Q., Yang, H., Liu, X., Dai, L., Ma, T., Qi, J., Wong, G., Peng, R., Liu, S., Li, J., Li, S., Song, J., Liu, J., He, J., Yuan, H., Xiong, Y., Liao, Y., Li, J., Yang, J., Tong, Z., Griffin, B., Bi, Y., Liang, M., Xu, X., Cheng, G., Wang, P., Qiu, X., Kobinger, G., Shi, Y., Yan, J., Gao, G.F.

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection