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- EMDB-71715: Cryo-EM structure of modified JEV virus E protein dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-71715
TitleCryo-EM structure of modified JEV virus E protein dimer
Map data
Sample
  • Complex: JEV virus E protein dimer
    • Protein or peptide: Genome polyprotein
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / double-stranded RNA binding / host cell surface / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / double-stranded RNA binding / host cell surface / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / viral translational frameshifting / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus non-structural protein NS2B / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. ...Flavivirus non-structural protein NS2B / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile.
Similarity search - Domain/homology
Biological speciesJapanese encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsGalkin A / Pozharski E / Li Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2025
Title: Rational design of flavivirus E protein vaccine optimizes immunogenicity and mitigates antibody dependent enhancement risk.
Authors: Yimeng Wang / Andrey Galkin / Xiaoran Shang / Alexander Marin / Shaohua Jin / Ting-Juan Ye / Shridhar Bale / Chi-I Chiang / Ananda Chowdhury / Agnes L Chenine / Ashley Turonis / Jack ...Authors: Yimeng Wang / Andrey Galkin / Xiaoran Shang / Alexander Marin / Shaohua Jin / Ting-Juan Ye / Shridhar Bale / Chi-I Chiang / Ananda Chowdhury / Agnes L Chenine / Ashley Turonis / Jack Greenhouse / Rebecca Stone / Jaclyn Wear / Swagata Kar / Hanne Andersen / Yan-Jang S Huang / Dana L Vanlandingham / Stephen Higgs / Rena G Lapidus / Thomas Fuerst / David J Weber / Richard T Wyatt / Christel Iffland / Theodore C Pierson / Alexander K Andrianov / Edwin Pozharski / Yuxing Li /
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 ...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.
History
DepositionJul 15, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71715.png

Downloads & links

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Map

FileDownload / File: emd_71715.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 320 pix.
= 284.48 Å		0.89 Å/pix.
x 320 pix.
= 284.48 Å		0.89 Å/pix.
x 320 pix.
= 284.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5004503 - 0.8603124
Average (Standard dev.)-0.0000055318487 (±0.014493684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 284.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71715_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71715_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : JEV virus E protein dimer

EntireName: JEV virus E protein dimer
Components
  • Complex: JEV virus E protein dimer
    • Protein or peptide: Genome polyprotein

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Supramolecule #1: JEV virus E protein dimer

SupramoleculeName: JEV virus E protein dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Japanese encephalitis virus

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Japanese encephalitis virus
Molecular weightTheoretical: 46.053715 KDa
Recombinant expressionOrganism: Drosophila (fruit flies)
SequenceString: GSGEQKLISE EDLGGGGSFN CLCMGNRDFI EGASGATWVD LVLEGDSCLT IMANDKPTLD VRMINIEASQ LAEVRSYCYH ASVTDISTV ARCPTTGEAH NEKRADSSYV CKQGFTDRGW CNGCGFFGKG SIDTCAKFSC TSKAIGRTIQ PENIKYKVGI F VHGTTTSE ...String:
GSGEQKLISE EDLGGGGSFN CLCMGNRDFI EGASGATWVD LVLEGDSCLT IMANDKPTLD VRMINIEASQ LAEVRSYCYH ASVTDISTV ARCPTTGEAH NEKRADSSYV CKQGFTDRGW CNGCGFFGKG SIDTCAKFSC TSKAIGRTIQ PENIKYKVGI F VHGTTTSE NHGNYSAQVG ASQAAKFTVT PNAPSVTLKL GDYGEVTLDC EPRSGLNTEA FYVMTVGSKS FLVHREWFHD LA LPWTSPS STAWRNRELL MEFEGAHATK QSVVALGSQE GGLHQALAGA IVVEYSSSVM LTSGHLKCRL KMDKLALKGT TYG MCTEKF SFAKNPVDTG HGTVVIELSY SGSDGPCKIP IVSVASLNDM TPVGRLVTVN PFVATSSANS KVLVEMEPPF GDSY IVVGR GDKQINHHWH KAGSGTGHHH HHH

UniProtKB: Genome polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 172829
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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