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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 virus
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 / double-stranded RNA binding / RNA helicase activity / 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
SourceJapanese encephalitis virus / virus / Japanese encephalitis
Methodsingle particle (icosahedral) reconstruction, at 4.3 Å resolution
AuthorsWang X / Zhu L
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 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
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5wsn
  • Surface level: 0.018
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5wsn
  • Imaged by Jmol
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3D viewer
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 package.

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
Origin000
Limit599599599
Spacing600600600
CellA=B=C: 810 Å
α=β=γ: 90 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
MassTheoretical: 11.8 MDa

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Component #1: virus, Japanese encephalitis virus

VirusName: Japanese encephalitis virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
MassTheoretical: 11.8 MDa
SpeciesSpecies: Japanese encephalitis virus / virus / Japanese encephalitis
Strain: P3
Source (engineered)Expression System: Chlorocebus aethiops / mammal / Grivet / Vector: no plasmids / Cell of expression system: vero
Source (natural)Host Species: Homo sapiens / human /
Shell #1Name of element: Envelope protein / Diameter: 500 Å / T number(triangulation number): 3

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Component #2: protein, E protein

ProteinName: E protein / Recombinant expression: No
MassTheoretical: 53.508684 kDa
Source (engineered)Expression System: Japanese encephalitis virus / virus / Japanese encephalitis
Strain: P3

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Component #3: protein, M protein

ProteinName: M protein / Recombinant expression: No
MassTheoretical: 8.250488 kDa
Source (engineered)Expression System: Japanese encephalitis virus / virus / Japanese encephalitis
Strain: P3

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Experimental details

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Sample preparation

Specimen stateparticle
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 - 3000 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2500

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Image processing

ProcessingMethod: single particle (icosahedral) 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 #1Refinement protocol: flexible / Target criteria: Correlation coefficient / Refinement space: REAL
Input PDB model: 3J57
Chain ID: 3J57_A

Overall bvalue: 120
Output model

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