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- EMDB-17946: Tick-borne encephalitis virus (strain Neudoerfl) immature particle -

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Basic information

Entry
Database: EMDB / ID: EMD-17946
TitleTick-borne encephalitis virus (strain Neudoerfl) immature particle
Map dataimmature particle of tick-borne encephalitis virus (strain Neudorfl)
Sample
  • Virus: Tick-borne encephalitis virus
    • Protein or peptide: Envelope protein E
    • Protein or peptide: Protein prM
Keywordsimmature particle / tick-borne / flavivirus / whole particle / VIRUS
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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. ...Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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 speciesTick-borne encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.02 Å
AuthorsFuzik T / Plevka P / Smerdova L / Novacek J
Funding support Czech Republic, 2 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLX22NPO5103 Czech Republic
CitationJournal: Sci Adv / Year: 2024
Title: The structure of immature tick-borne encephalitis virus supports the collapse model of flavivirus maturation.
Authors: Maria Anastasina / Tibor Füzik / Aušra Domanska / Lauri Ilmari Aurelius Pulkkinen / Lenka Šmerdová / Petra Pokorná Formanová / Petra Straková / Jiří Nováček / Daniel Růžek / ...Authors: Maria Anastasina / Tibor Füzik / Aušra Domanska / Lauri Ilmari Aurelius Pulkkinen / Lenka Šmerdová / Petra Pokorná Formanová / Petra Straková / Jiří Nováček / Daniel Růžek / Pavel Plevka / Sarah Jane Butcher /
Abstract: We present structures of three immature tick-borne encephalitis virus (TBEV) isolates. Our atomic models of the major viral components, the E and prM proteins, indicate that the pr domains of prM ...We present structures of three immature tick-borne encephalitis virus (TBEV) isolates. Our atomic models of the major viral components, the E and prM proteins, indicate that the pr domains of prM have a critical role in holding the heterohexameric prM3E3 spikes in a metastable conformation. Destabilization of the prM furin-sensitive loop at acidic pH facilitates its processing. The prM topology and domain assignment in TBEV is similar to the mosquito-borne Binjari virus, but is in contrast to other immature flavivirus models. These results support that prM cleavage, the collapse of E protein ectodomains onto the virion surface, the large movement of the membrane domains of both E and M, and the release of the pr fragment from the particle render the virus mature and infectious. Our work favors the collapse model of flavivirus maturation warranting further studies of immature flaviviruses to determine the sequence of events and mechanistic details driving flavivirus maturation.
History
DepositionJul 17, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17946.png

Downloads & links

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Map

FileDownload / File: emd_17946.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationimmature particle of tick-borne encephalitis virus (strain Neudorfl)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 512 pix.
= 800.256 Å		1.56 Å/pix.
x 512 pix.
= 800.256 Å		1.56 Å/pix.
x 512 pix.
= 800.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.563 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.02998823 - 0.06336373
Average (Standard dev.)0.0012087295 (±0.004272541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 800.256 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17946_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 of the gold standard reconstruction...

Fileemd_17946_half_map_1.map
Annotationhalf map 2 of the gold standard reconstruction of immature particle of tick-borne encephalitis virus (strain Neudorfl)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1 of the gold standard reconstruction...

Fileemd_17946_half_map_2.map
Annotationhalf map 1 of the gold standard reconstruction of immature particle of tick-borne encephalitis virus (strain Neudorfl)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tick-borne encephalitis virus

EntireName: Tick-borne encephalitis virus
Components
  • Virus: Tick-borne encephalitis virus
    • Protein or peptide: Envelope protein E
    • Protein or peptide: Protein prM

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Supramolecule #1: Tick-borne encephalitis virus

SupramoleculeName: Tick-borne encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Immature particles produced using tissue cell cultures
NCBI-ID: 11084 / Sci species name: Tick-borne encephalitis virus / Sci species strain: Neudoerfl / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Name: immature particle / Diameter: 600.0 Å

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Macromolecule #1: Envelope protein E

MacromoleculeName: Envelope protein E / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Tick-borne encephalitis virus / Strain: Neudoerfl
SequenceString: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGGT VCKRDQSDRG WGNHCGLFGK GSIVACVKAA CEAKKKATGH VYDANKIVYT VKVEPHTGDY VAANETHSGR KTASFTISSE ...String:
SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGGT VCKRDQSDRG WGNHCGLFGK GSIVACVKAA CEAKKKATGH VYDANKIVYT VKVEPHTGDY VAANETHSGR KTASFTISSE KTILTMGEYG DVSLLCRVAS GVDLAQTVIL ELDKTVEHLP TAWQVHRDWF NDLALPWKHE GAQNWNNAER LVEFGAPHAV KMDVYNLGDQ TGVLLKALAG VPVAHIEGTK YHLKSGHVTC EVGLEKLKMK GLTYTMCDKT KFTWKRAPTD SGHDTVVMEV TFSGTKPCRI PVRAVAHGSP DVNVAMLITP NPTIENNGGG FIEMQLPPGD NIIYVGELSH QWFQKGSSIG RVFQKTKKGI ERLTVIGEHA WDFGSAGGFL SSIGKAVHTV LGGAFNSIFG GVGFLPKLLL GVALAWLGLN MRNPTMSMSF LLAGGLVLAM TLGVGA

UniProtKB: Genome polyprotein

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Macromolecule #2: Protein prM

MacromoleculeName: Protein prM / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Tick-borne encephalitis virus / Strain: Neudoerfl
SequenceString:
TVRKERDGST VIRAEGKDAA TQVRVENGTC VILATDMGSW CDDSLSYECV TIDQGEEPVD VDCFCRNVDG VYLEYGRCGK QEGSRTRRSV LIPSHAQGEL TGRGHKWLEG DSLRTHLTRV EGWVWKNKLL ALAMVTVVWL TLESVVTRVA VLVVLLCLAP VYA

UniProtKB: Genome polyprotein

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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

Concentration2 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormulaName
20.0 mMTrisTrizma
120.0 mMNaClSodium Chloride
1.0 mMEDTA
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 280 K / Instrument: FEI VITROBOT MARK IV
Detailspurified immature particles of Tick-borne encephalitis virus

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 11246 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Details: collected in movie mode total 40 fractions per micrograph
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 156614
Details: autopicking performed by manually trained crYOLO neural network
Startup modelType of model: INSILICO MODEL / In silico model: SGD ab initio model / Details: RELION v 3.1
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 36236
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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