7BPK | pdb_00007bpk

Zika virus envelope protein mutant bound to mAb

• PDB DOI: https://doi.org/10.2210/pdb7BPK/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Zika virus, Homo sapiens
• Expression System: Escherichia coli, Mammalian expression vector Flag-MCS-pcDNA3.1, Mammalian expression vector BsrGI-MCS-pcDNA3.1
• Mutation(s): No 


• Deposited: 2020-03-23 Released: 2021-03-24 
• Deposition Author(s): Dai, L., Qi, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.268 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Protective Zika vaccines engineered to eliminate enhancement of dengue infection via immunodominance switch.

Dai, L., Xu, K., Li, J., Huang, Q., Song, J., Han, Y., Zheng, T., Gao, P., Lu, X., Yang, H., Liu, K., Xia, Q., Wang, Q., Chai, Y., Qi, J., Yan, J., Gao, G.F.

(2021) Nat Immunol 22: 958-968

• PubMed: 34267374 
• DOI: https://doi.org/10.1038/s41590-021-00966-6
• Primary Citation Related Structures: 
  7BPK, 7BQ5


• PubMed Abstract: 
  

  Antibody-dependent enhancement (ADE) is an important safety concern for vaccine development against dengue virus (DENV) and its antigenically related Zika virus (ZIKV) because vaccine may prime deleterious antibodies to enhance natural infections. Cross-reactive antibodies targeting the conserved fusion loop epitope (FLE) are known as the main sources of ADE. We design ZIKV immunogens engineered to change the FLE conformation but preserve neutralizing epitopes. Single vaccination conferred sterilizing immunity against ZIKV without ADE of DENV-serotype 1-4 infections and abrogated maternal-neonatal transmission in mice. Unlike the wild-type-based vaccine inducing predominately cross-reactive ADE-prone antibodies, B cell profiling revealed that the engineered vaccines switched immunodominance to dispersed patterns without DENV enhancement. The crystal structure of the engineered immunogen showed the dimeric conformation of the envelope protein with FLE disruption. We provide vaccine candidates that will prevent both ZIKV infection and infection-/vaccination-induced DENV ADE.

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Organizational Affiliation: 
• CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine and Laboratory Medicine, The First Affiliated Hospital, Hainan Medical University, Hainan, China. [e-mail].
Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Tropical Medicine and Laboratory Medicine, The First Affiliated Hospital, Hainan Medical University, Hainan, China.
University of Chinese Academy of Sciences, Beijing, China.
Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
Laboratory Animal Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.
Faculty of Health Sciences, University of Macau, Macau SAR, China.
CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. [e-mail].
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 141.99 kDa 
• Atom Count: 9,754 
• Modeled Residue Count: 1,278 
• Deposited Residue Count: 1,302 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein	A, B	416	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Z3L1 Heavy chain	C, E [auth H]	127	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IG c307_light_IGLV1-51_IGLJ2	D, F [auth L]	108	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for A0A5C2GK82 (Homo sapiens) Explore A0A5C2GK82  Go to UniProtKB:  A0A5C2GK82

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.268 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.462	α = 90
b = 103.79	β = 90
c = 205.818	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Dai, L., Qi, J., Gao, G.F.

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2021-10-20
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary