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- EMDB-6685: Structure of Japanese encephalitis virus -

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Basic information

Entry
Database: EMDB / ID: 6685
TitleStructure of Japanese encephalitis virus
Map dataCryo-EM map for the JEV particle
SampleJapanese encephalitis virusJapanese encephalitis:
virus / E protein / M protein
Function / homologyHelicase, C-terminal / 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 ...Helicase, C-terminal / 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 / Genome polyprotein, Flavivirus / Flavivirus NS3, petidase S7 / 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 / Envelope glycoprotein M superfamily, flavivirus / 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 NS4A / 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 / Flaviviral glycoprotein E, central domain, subdomain 2 / suppression by virus of host TYK2 activity / flavivirin / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / suppression by virus of host innate immune response / host cell endoplasmic reticulum / suppression by virus of host STAT1 activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / ATP-dependent helicase activity / host cell membrane / suppression by virus of host type I interferon-mediated signaling pathway / RNA helicase activity / RNA helicase / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / clathrin-dependent endocytosis of virus by host cell / viral RNA genome replication / fusion of virus membrane with host endosome membrane / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / extracellular region / ATP binding / metal ion binding / Genome polyprotein / Genome polyprotein / Polyprotein
Function and homology information
SourceJapanese encephalitis virus
Methodsingle particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsWang X / Zhu L / Li S / Yuan S / Qin C / Fry EE / Stuart ID / 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 ReportPDB-ID: 5wsn

SummaryFull reportAbout validation report
DateDeposition: Dec 7, 2016 / Header (metadata) release: Dec 21, 2016 / Map release: May 17, 2017 / Last update: May 17, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • 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 models: PDB-5wsn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6685.map.gz (map file in CCP4 format, 864001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
1.35 Å/pix.
= 810. Å
600 pix
1.35 Å/pix.
= 810. Å
600 pix
1.35 Å/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
Contour Level:0.018 (by author), 0.018 (movie #1):
Minimum - Maximum-0.023495236 - 0.0602432
Average (Standard dev.)0.00066363683 (0.0041144555)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin0.00.00.0
Limit599.0599.0599.0
Spacing600600600
CellA=B=C: 810.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 / Number of components: 3

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Component #1: virus, Japanese encephalitis virus

VirusName: Japanese encephalitis virusJapanese encephalitis / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
MassTheoretical: 11.8 MDa
SpeciesSpecies: Japanese encephalitis virus / Strain: P3
Source (engineered)Expression System: Chlorocebus aethiops (grivet) / Vector: no plasmids / Cell of expression system: vero
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: Envelope protein / Diameter: 500.0 Å / T number(triangulation number): 3

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Component #2: protein, E protein

ProteinName: E protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 53.508684 kDa
SourceSpecies: Japanese encephalitis virus / Strain: P3
Source (engineered)Expression System: Chlorocebus aethiops (grivet)
Source (natural)Organ or tissue: Homo sapiens

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Component #3: protein, M protein

ProteinName: M protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 8.250488 kDa
SourceSpecies: Japanese encephalitis virus / Strain: P3
Source (engineered)Expression System: Chlorocebus aethiops (grivet)
Source (natural)Organ or tissue: Homo sapiens

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2.5 mg/ml / Buffer solution: PBS buffer / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 95 % / Details: blot for 3 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.2 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2500

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 15260
3D reconstructionSoftware: Relion / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 3J57
Chain ID: A

Overall bvalue: 12
Output model

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