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- EMDB-6685: Structure of Japanese encephalitis virus -

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Basic information

Entry
Database: EMDB / ID: EMD-6685
TitleStructure of Japanese encephalitis virus
Map dataCryo-EM map for the JEV particle
Sample
  • Virus: Japanese encephalitis virus
    • Protein or peptide: E protein
    • Protein or peptide: M protein
KeywordsJapanese encephalitis virus / Viral entry / Flavivirus / Neurotropism / VIRUS
Function / homology
Function and homology information


flavivirin / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase ...flavivirin / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell surface / 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 / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / 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 / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / 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 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / 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 envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Polyprotein
Similarity search - Component
Biological speciesJapanese encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWang X / Zhu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570717 China
CitationJournal: Nat Commun / Year: 2017
Title: Near-atomic structure of Japanese encephalitis virus reveals critical determinants of virulence and stability.
Authors: Xiangxi Wang / Shi-Hua Li / Ling Zhu / Qing-Gong Nian / Shuai Yuan / Qiang Gao / Zhongyu Hu / Qing Ye / Xiao-Feng Li / Dong-Yang Xie / Neil Shaw / Junzhi Wang / Thomas S Walter / Juha T ...Authors: Xiangxi Wang / Shi-Hua Li / Ling Zhu / Qing-Gong Nian / Shuai Yuan / Qiang Gao / Zhongyu Hu / Qing Ye / Xiao-Feng Li / Dong-Yang Xie / Neil Shaw / Junzhi Wang / Thomas S Walter / Juha T Huiskonen / Elizabeth E Fry / Cheng-Feng Qin / David I Stuart / Zihe Rao /
Abstract: Although several different flaviviruses may cause encephalitis, Japanese encephalitis virus is the most significant, being responsible for thousands of deaths each year in Asia. The structural and ...Although several different flaviviruses may cause encephalitis, Japanese encephalitis virus is the most significant, being responsible for thousands of deaths each year in Asia. The structural and molecular basis of this encephalitis is not fully understood. Here, we report the cryo-electron microscopy structure of mature Japanese encephalitis virus at near-atomic resolution, which reveals an unusual "hole" on the surface, surrounded by five encephalitic-specific motifs implicated in receptor binding. Glu138 of E, which is highly conserved in encephalitic flaviviruses, maps onto one of these motifs and is essential for binding to neuroblastoma cells, with the E138K mutation abrogating the neurovirulence and neuroinvasiveness of Japanese encephalitis virus in mice. We also identify structural elements modulating viral stability, notably Gln264 of E, which, when replaced by His264 strengthens a hydrogen-bonding network, leading to a more stable virus. These studies unveil determinants of neurovirulence and stability in Japanese encephalitis virus, opening up new avenues for therapeutic interventions against neurotropic flaviviruses.Japanese encephalitis virus (JEV) is a Flavivirus responsible for thousands of deaths every year for which there are no specific anti-virals. Here, Wang et al. report the cryo-EM structure of mature JEV at near-atomic resolution and identify structural elements that modulate stability and virulence.
History
DepositionDec 7, 2016-
Header (metadata) releaseDec 21, 2016-
Map releaseMay 17, 2017-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5wsn
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5wsn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6685.png

Downloads & links

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Map

FileDownload / File: emd_6685.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map for the JEV particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 600 pix.
= 810. Å		1.35 Å/pix.
x 600 pix.
= 810. Å		1.35 Å/pix.
x 600 pix.
= 810. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.023495236 - 0.0602432
Average (Standard dev.)0.00066363683 (±0.0041144555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 810.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z810.000810.000810.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0230.0600.001

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Supplemental data

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Sample components

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Entire : Japanese encephalitis virus

EntireName: Japanese encephalitis virus
Components
  • Virus: Japanese encephalitis virus
    • Protein or peptide: E protein
    • Protein or peptide: M protein

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Supramolecule #1: Japanese encephalitis virus

SupramoleculeName: Japanese encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11072 / Sci species name: Japanese encephalitis virus / Sci species strain: P3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.8 MDa
Virus shellShell ID: 1 / Name: Envelope protein / Diameter: 500.0 Å / T number (triangulation number): 3

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Macromolecule #1: E protein

MacromoleculeName: E protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Japanese encephalitis virus / Strain: P3 / Organ: Homo sapiens
Molecular weightTheoretical: 53.508684 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: FNCLGMGNRD FIEGASGATW VDLVLEGDSC LTIMANDKPT LDVRMINIEA SQLAEVRSYC YHASVTDIST VARCPMTGEA HNEKRADSS YVCKQGFTDR GWGNGCGLFG KGSIDTCAKF SCTSKAIGRT IQPENIKYEV GIFVHGTTTS ENHGNYSAQV G ASQAAKFT ...String:
FNCLGMGNRD FIEGASGATW VDLVLEGDSC LTIMANDKPT LDVRMINIEA SQLAEVRSYC YHASVTDIST VARCPMTGEA HNEKRADSS YVCKQGFTDR GWGNGCGLFG KGSIDTCAKF SCTSKAIGRT IQPENIKYEV GIFVHGTTTS ENHGNYSAQV G ASQAAKFT VTPNAPSITL KLGDYGEVTL DCEPRSGLNT EAFYVMTVGS KSFLVHREWF HDLALPWTPP SSTAWRNREL LM EFEEAHA TKQSVVALGS QEGGLHQALA GAIVVEYSSS VKLTSGHLKC RLKMDKLALK GTTYGMCTGK FSFAKNPADT GHG TVVIEL SYSGSDGPCK IPIVSVASLN DMTPVGRLVT VNPFVATSSA NSKVLVEMEP PFGDSYIVVG RGDKQINHHW HKAG STLGK AFLTTLKGAQ RLAALGDTAW DFGSIGGVFN SIGKAVHQVF GGAFRTLFGG MSWITQGLMG ALLLWMGVNA RDRSI ALAF LATGGVLLFL ATNVHA

UniProtKB: Genome polyprotein

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Macromolecule #2: M protein

MacromoleculeName: M protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Japanese encephalitis virus / Strain: P3 / Organ: Homo sapiens
Molecular weightTheoretical: 8.250488 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString:
SVSVQTHGES SLVNKTETWL DSTKATRYLM KTENWIIRNP GYAFLAAVLG WMLGSNNGQR VVFTILLLLV APAY

UniProtKB: 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

Concentration2.5 mg/mL
BufferpH: 7.4 / Details: PBS buffer
GridModel: C-flat / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III / Details: blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-18 / Number grids imaged: 5 / Number real images: 2500 / Average exposure time: 1.5 sec. / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 22000
Startup modelType of model: EMDB MAP
EMDB ID:

5520

Final reconstructionNumber classes used: 120 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 15260
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber classes: 150 / Avg.num./class: 120 / Software - Name: RELION (ver. 1.3)

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Atomic model buiding 1

Initial modelPDB ID:

3j57
PDB Unreleased entry


Chain - Chain ID: A / Chain - Residue range: 1-395 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 120 / Target criteria: Correlation coefficient
Output model

PDB-5wsn:
Structure of Japanese encephalitis virus

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