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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: EMD-3752
TitleThe cryo-EM structure of Tick-borne encephalitis virus mature particle
Map dataMature tick-borne encephalitis virus particle
Sample
  • Virus: Tick-borne encephalitis virus (strain HYPR)
    • Protein or peptide: Envelope proteinViral envelope
    • Protein or peptide: Small envelope protein M
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesTBEV (virus) / Tick-borne encephalitis virus (strain HYPR)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFuzik T / Plevka P
Funding support Czech Republic, Germany, 3 items
OrganizationGrant numberCountry
European Research Council355855
Czech Science Foundation17-02196S Czech Republic
European Molecular Biology OrganizationIG3041 Germany
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 /
Abstract: Tick-borne encephalitis virus (TBEV) causes 13,000 cases of human meningitis and encephalitis annually. However, the structure of the TBEV virion and its interactions with antibodies are unknown. ...Tick-borne encephalitis virus (TBEV) causes 13,000 cases of human meningitis and encephalitis annually. However, the structure of the TBEV virion and its interactions with antibodies are unknown. Here, we present cryo-EM structures of the native TBEV virion and its complex with Fab fragments of neutralizing antibody 19/1786. Flavivirus genome delivery depends on membrane fusion that is triggered at low pH. The virion structure indicates that the repulsive interactions of histidine side chains, which become protonated at low pH, may contribute to the disruption of heterotetramers of the TBEV envelope and membrane proteins and induce detachment of the envelope protein ectodomains from the virus membrane. The Fab fragments bind to 120 out of the 180 envelope glycoproteins of the TBEV virion. Unlike most of the previously studied flavivirus-neutralizing antibodies, the Fab fragments do not lock the E-proteins in the native-like arrangement, but interfere with the process of virus-induced membrane fusion.
History
DepositionJun 6, 2017-
Header (metadata) releaseJul 12, 2017-
Map releaseFeb 7, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

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

emd_3752.png

Downloads & links

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Map

FileDownload / File: emd_3752.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMature tick-borne encephalitis virus particle
Voxel sizeX=Y=Z: 1.45 Å
Density
Contour LevelBy AUTHOR: 2.8 / Movie #1: 2.8
Minimum - Maximum-7.8213224 - 14.608998
Average (Standard dev.)0.731232700 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 522.0 Å
α=β=γ: 90.0 °

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)
Components
  • Virus: Tick-borne encephalitis virus (strain HYPR)
    • Protein or peptide: Envelope proteinViral envelope
    • Protein or peptide: Small envelope protein M
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

SupramoleculeName: Tick-borne encephalitis virus (strain HYPR) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 70733
Sci species name: Tick-borne encephalitis virus (strain HYPR)
Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: No
Molecular weightTheoretical: 22 MDa
Virus shellShell ID: 1 / Name: Mature particle / Diameter: 500.0 Å / T number (triangulation number): 3

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Macromolecule #1: Envelope protein

MacromoleculeName: Envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: flavivirin
Source (natural)Organism: TBEV (virus) / Strain: Hypr
Molecular weightTheoretical: 53.667418 KDa
SequenceString: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAQTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGG TVCKRDQSDR GWGNHCGLFG KGSIVACVKA ACEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS ...String:
SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAQTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGG TVCKRDQSDR GWGNHCGLFG KGSIVACVKA ACEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS SEKTILTMGE YGDVSLLCRV ASGVDLAQTV ILELDKTVEH LPTAWQVHRD WFNDLALPWK HEGARNWNNA ER LVEFGAP HAVKMDVYNL GDQTGVLLKA LAGVPVAHIE GTKYHLKSGH VTCEVGLEKL KMKGLTYTMC DKTKFTWKRA PTD SGHDTV VMEVTFSGTK PCRIPVRAVA HGSPDVNVAM LITPNPTIEN NGGGFIEMQL PPGDNIIYVG ELSYQWFQKG SSIG RVFQK TKKGIERLTV IGEHAWDFGS AGGFLSSIGK ALHTVLGGAF NSIFGGVGFL PKLLLGVALA WLGLNMRNPT MSMSF LLAG VLVLAMTLGV GA

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Macromolecule #2: Small envelope protein M

MacromoleculeName: Small envelope protein M / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: flavivirin
Source (natural)Organism: TBEV (virus) / Strain: Hypr
Molecular weightTheoretical: 8.339867 KDa
SequenceString:
SVLIPSHAQG ELTGRGHKWL EGDSLRTHLT RVEGWVWKNR LLALAMVTVV WLTLESVVTR VAVLVVLLCL APVYA

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.5
Component:
ConcentrationFormulaName
20.0 mMTrisTris
120.0 mMNaClSodium chloridesodium cloride
1.0 mMEDTAEthylenediaminetetraacetic acidEthylenediaminetetraacetic acid
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: NITROGEN / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: Wait time: 10 s Blot time: 2 s Blot force: -2 Drain time: 0 s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 5426 / Average exposure time: 0.5 sec. / Average electron dose: 22.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 19111
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 7.5 degrees
Software - Name: RELION (ver. 1.4) / Software - details: 3dautorefine
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) / Software - details: 3dautorefine
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Software - details: 3dautorefine / Number images used: 11882
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2svb


Chain - Chain ID: A / Chain - Residue range: 1-395
DetailsAn 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.
RefinementSpace: RECIPROCAL / Protocol: OTHER
Output model

PDB-5o6a:
The cryo-EM structure of Tick-borne encephalitis virus mature particle

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