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- EMDB-3752: The cryo-EM structure of Tick-borne encephalitis virus mature particle -

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Basic information

Entry
Database: EMDB / ID: 3752
TitleThe cryo-EM structure of Tick-borne encephalitis virus mature particle
Map dataMature tick-borne encephalitis virus particle
SampleTick-borne encephalitis virus (strain HYPR):
virus / Envelope proteinViral envelope / Small envelope protein M / ligand
Function / homologyFlavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flaviviral glycoprotein E, central domain, subdomain 2 / RNA-directed RNA polymerase, flavivirus ...Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flaviviral glycoprotein E, central domain, subdomain 2 / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS2B / S-adenosyl-L-methionine-dependent methyltransferase / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / Flavivirus non-structural protein NS1 / Flaviviral glycoprotein E, central domain, subdomain 1 / Helicase, C-terminal / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus glycoprotein central and dimerisation domain / Flavivirus polyprotein propeptide / 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 non-structural protein NS4A / Flaviviral glycoprotein E, dimerisation domain / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / 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 / DEAD box, Flavivirus / 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
Function and homology information
SourceTick-borne encephalitis virus (strain Hypr)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsFuzik T / Plevka P
CitationJournal: Nat Commun / Year: 2018
Title: Structure of tick-borne encephalitis virus and its neutralization by a monoclonal antibody.
Authors: Tibor Füzik / Petra Formanová / Daniel Růžek / Kentaro Yoshii / Matthias Niedrig / Pavel Plevka
Validation ReportPDB-ID: 5o6a

SummaryFull reportAbout validation report
DateDeposition: Jun 6, 2017 / Header (metadata) release: Jul 12, 2017 / Map release: Feb 7, 2018 / Last update: Mar 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5o6a
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5o6a
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3752.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
360 pix
1.45 Å/pix.
= 522. Å
360 pix
1.45 Å/pix.
= 522. Å
360 pix
1.45 Å/pix.
= 522. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour Level:2.8 (by author), 2.8 (movie #1):
Minimum - Maximum-7.8213224 - 14.608998
Average (Standard dev.)7.31233E-10 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions360360360
Origin-180-180-180
Limit179179179
Spacing360360360
CellA=B=C: 522 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z522.000522.000522.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-180
NX/NY/NZ360360360
MAP C/R/S312
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-7.82114.6090.000

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Supplemental data

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Sample components

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Entire Tick-borne encephalitis virus (strain HYPR)

EntireName: Tick-borne encephalitis virus (strain HYPR) / Number of components: 4
MassTheoretical: 22 MDa

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Component #1: virus, Tick-borne encephalitis virus (strain HYPR)

VirusName: Tick-borne encephalitis virus (strain HYPR) / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: SEROTYPE
MassTheoretical: 22 MDa
SpeciesSpecies: Tick-borne encephalitis virus (strain HYPR)
Shell #1Name of element: Mature particle / Diameter: 500 Å / T number(triangulation number): 3

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Component #2: protein, Envelope protein

ProteinName: Envelope proteinViral envelope / Recombinant expression: No
MassTheoretical: 53.667418 kDa
SourceSpecies: Tick-borne encephalitis virus (strain Hypr) / Strain: Hypr

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Component #3: protein, Small envelope protein M

ProteinName: Small envelope protein M / Recombinant expression: No
MassTheoretical: 8.339867 kDa
SourceSpecies: Tick-borne encephalitis virus (strain Hypr) / Strain: Hypr

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Component #4: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %
Details: Wait time: 10 s Blot time: 2 s Blot force: -2 Drain time: 0 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 22 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000 X (nominal), 75000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5426 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 11882
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: RECIPROCAL
Details: An initial model was generated based on the known crystal structure of the ecto-domain (PDB:1SVB), Dengue virus type 2 and the Zika virus (PDB:5IRE,3J27) using the program Modeller. The model was rigid-body fitted to the electron density map of the TBEV particle using the program Chimera. Subsequently, the structure was manually corrected using the program Coot, followed by real-space refinement in Phenix and reciprocal space refinement in Refmac5.
Input PDB model: 2SVB
Chain ID: 2SVB_A
Output model

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