9PL9 | pdb_00009pl9

Cryo-EM structure of modified JEV virus E protein dimer

• PDB DOI: https://doi.org/10.2210/pdb9PL9/pdb
• EM Map EMD-71715: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Japanese encephalitis virus
• Expression System: Drosophila
• Mutation(s): No 


• Deposited: 2025-07-15 Released: 2026-01-21 
• Deposition Author(s): Galkin, A., Pozharski, E., Li, Y.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Rational design of flavivirus E protein vaccine optimizes immunogenicity and mitigates antibody dependent enhancement risk.

Wang, Y., Galkin, A., Shang, X., Marin, A., Jin, S., Ye, T.J., Bale, S., Chiang, C.I., Chowdhury, A., Chenine, A.L., Turonis, A., Greenhouse, J., Stone, R., Wear, J., Kar, S., Andersen, H., Huang, Y.S., Vanlandingham, D.L., Higgs, S., Lapidus, R.G., Fuerst, T., Weber, D.J., Wyatt, R.T., Iffland, C., Pierson, T.C., Andrianov, A.K., Pozharski, E., Li, Y.

(2025) Nat Commun 16: 11558-11558

• PubMed: 41429771 
• DOI: https://doi.org/10.1038/s41467-025-67447-4
• Primary Citation of Related Structures:  
  9OD2, 9PL9, 9PM6


• PubMed Abstract: 
  

  Flaviviruses are a family of related viruses that cause substantial global morbidity and mortality. Vaccination against one flavivirus can sometimes exacerbate disease caused by related viruses through antibody-dependent enhancement (ADE) or interfere with the efficacy of subsequent vaccines. To address this challenge, we develop a vaccine strategy by introducing G5C/G102C mutations into the flavivirus envelope (E) glycoprotein. These mutations promote E dimerization through the formation of an inter-chain disulfide bond that conceals the immunodominant and ADE-prone fusion loop epitope (FLE). We validate this design on E proteins from multiple flaviviruses through biochemical, antigenic, and structural analyses. The resulting vaccine candidate, CC_FLE sE, derived from the Zika virus (ZIKV) and formulated with an advanced supramolecular adjuvant, provides significant protection in female mice challenged with ZIKV and prevents ADE caused by a related flavivirus, Dengue virus. In genetically modified mice expressing diverse human immunoglobulin loci, ZIKV CC_FLE sE induces robust neutralizing antibody responses targeting key ZIKV E protein epitopes, including the E-dimer-dependent epitope (EDE), indicating that ZIKV CC_FLE sE can elicit protective antibody responses within the human naïve B cell repertoire. Therefore, CC_FLE sE represents a promising strategy for developing flavivirus vaccines that minimize ADE risk while maintaining high protective efficacy.

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Organizational Affiliation: 
• Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.
ReVacc, Inc., Cambridge, MA, USA.
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
Integrated BioTherapeutics, Inc., Rockville, MD, USA.
BIOQUAL, Inc., Rockville, MD, USA.
Biosecurity Research Institute and Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
Center for Biomolecular Therapeutics, Rockville, MD, USA.
Center for Biomolecular Therapeutic, Baltimore, MD, USA.
OmniAb, Inc., Emeryville, CA, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
Institute for Bioscience and Biotechnology Research, Rockville, MD, USA. [e-mail].
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA. [e-mail].
Center for Biomolecular Therapeutics, Rockville, MD, USA. [e-mail].
Center for Biomolecular Therapeutic, Baltimore, MD, USA. [e-mail].
Institute for Bioscience and Biotechnology Research, Rockville, MD, USA. [e-mail].
Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA. [e-mail].
Center for Biomolecular Therapeutics, Rockville, MD, USA. [e-mail].
Center for Biomolecular Therapeutic, Baltimore, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 93.6 kDa 
• Atom Count: 6,160 
• Modeled Residue Count: 802 
• Deposited Residue Count: 856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	428	Japanese encephalitis virus	Mutation(s): 0
UniProt
Find proteins for A0A8E6P5G2 (Japanese encephalitis virus) Explore A0A8E6P5G2  Go to UniProtKB:  A0A8E6P5G2
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D [auth G]	4		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.18 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Galkin, A., Pozharski, E., Li, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release