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- PDB-5wsn: Structure of Japanese encephalitis virus -

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Basic information

Entry
Database: PDB / ID: 5wsn
TitleStructure of Japanese encephalitis virus
Components
  • E protein
  • M protein
KeywordsVIRUS / Japanese encephalitis virus / Viral entry / Flavivirus / Neurotropism
Function/homologysuppression by virus of host TYK2 activity / Flavivirin / mRNA (guanine-N7-)-methyltransferase / mRNA (nucleoside-2'-O-)-methyltransferase / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus capsid protein C / Envelope glycoprotein M, flavivirus / Flavivirus capsid protein C ...suppression by virus of host TYK2 activity / Flavivirin / mRNA (guanine-N7-)-methyltransferase / mRNA (nucleoside-2'-O-)-methyltransferase / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus capsid protein C / Envelope glycoprotein M, flavivirus / Flavivirus capsid protein C / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / RNA-directed RNA polymerase, flavivirus / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus NS3, petidase S7 / Flavivirus non-structural protein NS1 / Flavivirus non-structural Protein NS1 / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / suppression by virus of host STAT2 activity / Flavivirus RNA-directed RNA polymerase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Ribosomal RNA methyltransferase FtsJ domain / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domains / mRNA (nucleoside-2'-O-)-methyltransferase activity / serine-type exopeptidase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity / FtsJ-like methyltransferase / Flavivirus glycoprotein, immunoglobulin-like domain / host cell endoplasmic reticulum membrane / DEAD box, Flavivirus / ATP-dependent helicase activity / Flavivirus DEAD domain / host cell perinuclear region of cytoplasm / RNA helicase activity / double-stranded RNA binding / suppression by virus of host type I interferon-mediated signaling pathway / RNA helicase / Superfamilies 1 and 2 helicase C-terminal domain profile. / viral capsid / nucleoside-triphosphatase / RNA-directed RNA polymerase / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Helicase, C-terminal / induction by virus of host autophagy / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Immunoglobulin E-set / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral RNA genome replication / S-adenosyl-L-methionine-dependent methyltransferase / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / virion attachment to host cell / host cell nucleus / virion membrane / Peptidase S1, PA clan / structural molecule activity / serine-type endopeptidase activity / regulation of transcription, DNA-templated / P-loop containing nucleoside triphosphate hydrolase / transcription, DNA-templated / integral component of membrane / extracellular region / ATP binding / metal ion binding / Genome polyprotein / Genome polyprotein / Polyprotein
Function and homology information
Specimen sourceJapanese encephalitis virus / Japanese encephalitis / virus
MethodElectron microscopy (4.3 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsWang, X. / Zhu, L. / Li, S. / Yuan, S. / Qin, C. / Fry, E.E. / Stuart, I.D. / Rao, Z.
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 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 7, 2016 / Release: May 17, 2017

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein


Theoretical massNumber of molelcules
Total (without water)185,2786
Polyers185,2786
Non-polymers00
Water0
1
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 60


Theoretical massNumber of molelcules
Total (without water)11,116,651360
Polyers11,116,651360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 5


  • icosahedral pentamer
  • 926 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)926,38830
Polyers926,38830
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 6


  • icosahedral 23 hexamer
  • 1.11 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,111,66536
Polyers1,111,66536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
x 60


  • crystal asymmetric unit, crystal frame
  • 11.1 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)11,116,651360
Polyers11,116,651360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60

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Components

#1: Protein/peptide E protein


Mass: 53508.684 Da / Num. of mol.: 3
Source: (gene. exp.) Japanese encephalitis virus / Japanese encephalitis / virus
Strain: P3 / Organ: Homo sapiens
Cell line (production host): green monkey kidney (Vero) cells
Production host: Chlorocebus aethiops / References: UniProt:A1E4C6
#2: Protein/peptide M protein


Mass: 8250.488 Da / Num. of mol.: 3
Source: (gene. exp.) Japanese encephalitis virus / Japanese encephalitis / virus
Strain: P3 / Organ: Homo sapiens
Cell line (production host): green monkey kidney (Vero) cells
Production host: Chlorocebus aethiops / References: UniProt:Q82863, UniProt:P27395*PLUS
Sequence detailsThis sequence is derived from Japanese encephalitis virus (P3 strain).

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Japanese encephalitis virus / Type: VIRUS / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 11.8 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Japanese encephalitis virus / Strain: P3
Source (recombinant)Cell: vero / Organism: Chlorocebus aethiops / Plasmid: no plasmids
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Envelope protein / Diameter: 500 Å / Triangulation number (T number): 3
Buffer solutionDetails: PBS buffer / pH: 7.4
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 kelvins / Details: blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 2 mm / C2 aperture diameter: 100 mm
Specimen holderSpecimen holder model: OTHER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 5 / Number of real images: 2500
Image scansDimension width: 3710 / Dimension height: 3710 / Movie frames/image: 25 / Used frames/image: 2-18

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EMAN2.0IMAGE ACQUISITIONEMAN2 e2boxer.py was used to automatically select particle images
3Relion1.3IMAGE ACQUISITIONRelion was used to reconstruct 3D structures
5Gctf5.0CTF CORRECTION
8CHIMERA2.0MODEL FITTING
10RelionINITIAL EULER ASSIGNMENT
11Relion1.3FINAL EULER ASSIGNMENT
12Relion1.3CLASSIFICATION
13Relion1.3RECONSTRUCTION
14PHENIX3.OMODEL REFINEMENT
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 22000
SymmetryPoint symmetry: I
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 15260 / Number of class averages: 120 / Symmetry type: POINT
Atomic model buildingOverall b value: 120 / Ref protocol: AB INITIO MODEL / Ref space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 3J57
Pdb chain ID: A / Pdb chain residue range: 1-395
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01113367
ELECTRON MICROSCOPYf_angle_d1.08018150
ELECTRON MICROSCOPYf_dihedral_angle_d8.96110527
ELECTRON MICROSCOPYf_chiral_restr0.0512075
ELECTRON MICROSCOPYf_plane_restr0.0062297

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