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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 / homologyFlavivirus NS3, petidase S7 / Flavivirus non-structural protein NS2A / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus ...Flavivirus NS3, petidase S7 / Flavivirus non-structural protein NS2A / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS4B / Helicase, C-terminal / Genome polyprotein, Flavivirus / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / DEAD box, Flavivirus / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Helicase superfamily 1/2, ATP-binding domain / Flavivirus non-structural protein NS4A / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus NS2B domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Flavivirus DEAD domain / Flavivirus glycoprotein, immunoglobulin-like domain / FtsJ-like methyltransferase / Flavivirus polyprotein propeptide / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS2A / Flavivirus envelope glycoprotein M / Flavivirus capsid protein C / Flavivirus non-structural protein NS2B / Flavivirus RNA-directed RNA polymerase / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus non-structural Protein NS1 / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Envelope glycoprotein M superfamily, flavivirus / Flaviviral glycoprotein E, central domain, subdomain 2 / suppression by virus of host TYK2 activity / Flavivirin / mRNA (guanine-N7-)-methyltransferase / mRNA (nucleoside-2'-O-)-methyltransferase / suppression by virus of host STAT2 activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / ATP-dependent helicase activity / 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 / nucleoside-triphosphatase / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / serine-type endopeptidase activity / regulation of transcription, DNA-templated / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.3 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 7, 2016 / Release: May 17, 2017

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Structure visualization

Movie
  • 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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  • Superimposition on EM map
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Structure viewerMolecule:
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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 / Strain: P3 / Organ: Homo sapiens
Cell line (production host): green monkey kidney (Vero) cells
Production host: Chlorocebus aethiops (grivet) / References: UniProt: A1E4C6
#2: Protein/peptide M protein


Mass: 8250.488 Da / Num. of mol.: 3 / Source: (gene. exp.) Japanese encephalitis virus / Strain: P3 / Organ: Homo sapiens
Cell line (production host): green monkey kidney (Vero) cells
Production host: Chlorocebus aethiops (grivet) / 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 reconstruction

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Sample preparation

ComponentName: Japanese encephalitis virusJapanese encephalitis / Type: VIRUS / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 11.8 MDa / Experimental value: NO
Source (natural)Organism: Japanese encephalitis virus / Strain: P3
Source (recombinant)Cell: vero / Organism: Chlorocebus aethiops (grivet) / Plasmid: no plasmids
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Envelope proteinViral envelope / Diameter: 500 nm / 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 FIELDBright-field microscopy / 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 scansWidth: 3710 / 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
13Relion1.33D reconstruction
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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