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- EMDB-14512: Tick-borne encephalitis virus Kuutsalo-14 -

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Basic information

Entry
Database: EMDB / ID: EMD-14512
TitleTick-borne encephalitis virus Kuutsalo-14
Map dataAutomatically locally sharpened map used for model buidling. Sharpened using Xmipp Localdeblursharpening.
Sample
  • Virus: Tick-borne encephalitis virus
    • Protein or peptide: Envelope protein E
    • Protein or peptide: Small envelope protein M
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Keywordsvirion / membrane protein / glycoprotein / 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 (WESTERN SUBTYPE) / Tick-borne encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPulkkinen LIA / Barrass SV / Anastasina M / Butcher SJ
Funding support Finland, European Union, Sweden, 9 items
OrganizationGrant numberCountry
University of Helsinki Finland
University of Helsinki Finland
University of Helsinki Research Foundation Finland
H2020 Marie Curie Actions of the European Commission799929European Union
H2020 Marie Curie Actions of the European Commission765042European Union
Swedish Research Council2018-05851 Sweden
Academy of Finland315950 Finland
Sigrid Juselius Foundation95-7202-38 Finland
Jane and Aatos Erkko Foundation Finland
CitationJournal: Viruses / Year: 2022
Title: Molecular Organisation of Tick-Borne Encephalitis Virus.
Authors: Lauri I A Pulkkinen / Sarah V Barrass / Aušra Domanska / Anna K Överby / Maria Anastasina / Sarah J Butcher /
Abstract: Tick-borne encephalitis virus (TBEV) is a pathogenic, enveloped, positive-stranded RNA virus in the family . Structural studies of flavivirus virions have primarily focused on mosquito-borne species, ...Tick-borne encephalitis virus (TBEV) is a pathogenic, enveloped, positive-stranded RNA virus in the family . Structural studies of flavivirus virions have primarily focused on mosquito-borne species, with only one cryo-electron microscopy (cryo-EM) structure of a tick-borne species published. Here, we present a 3.3 Å cryo-EM structure of the TBEV virion of the Kuutsalo-14 isolate, confirming the overall organisation of the virus. We observe conformational switching of the peripheral and transmembrane helices of M protein, which can explain the quasi-equivalent packing of the viral proteins and highlights their importance in stabilising membrane protein arrangement in the virion. The residues responsible for M protein interactions are highly conserved in TBEV but not in the structurally studied Hypr strain, nor in mosquito-borne flaviviruses. These interactions may compensate for the lower number of hydrogen bonds between E proteins in TBEV compared to the mosquito-borne flaviviruses. The structure reveals two lipids bound in the E protein which are important for virus assembly. The lipid pockets are comparable to those recently described in mosquito-borne Zika, Spondweni, Dengue, and Usutu viruses. Our results thus advance the understanding of tick-borne flavivirus architecture and virion-stabilising interactions.
History
DepositionMar 7, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14512.png

Downloads & links

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Map

FileDownload / File: emd_14512.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAutomatically locally sharpened map used for model buidling. Sharpened using Xmipp Localdeblursharpening.
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 640 pix.
= 691.2 Å		1.08 Å/pix.
x 640 pix.
= 691.2 Å		1.08 Å/pix.
x 640 pix.
= 691.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0029738715 - 0.1761272
Average (Standard dev.)0.00062224525 (±0.005540728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-319-319-319
Dimensions640640640
Spacing640640640
CellA=B=C: 691.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Minimally sharpened map used for model building. B factor -5 A^2.

Fileemd_14512_additional_1.map
AnnotationMinimally sharpened map used for model building. B factor -5 A^2.
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_14512_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_14512_half_map_2.map
Projections & Slices
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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: Small envelope protein M
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Tick-borne encephalitis virus

SupramoleculeName: Tick-borne encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Virus was produced in SK-N-SH cells, purified, and inactivated with UV-C.
NCBI-ID: 11088 / Sci species name: Tick-borne encephalitis virus / Sci species strain: Neudoerfl / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope protein E

MacromoleculeName: Envelope protein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tick-borne encephalitis virus (WESTERN SUBTYPE) / Strain: Neudoerfl
Molecular weightTheoretical: 53.55827 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGG TVCKRDQSDR GWGNHCGLFG KGSIVACVKA ACEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS ...String:
SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDAIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQGG TVCKRDQSDR GWGNHCGLFG KGSIVACVKA ACEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS SEKTILTMGE YGDVSLLCRV ASGVDLAQTV ILELDKTVEH LPTAWQVHRD WFNDLALPWK HEGAQNWNNA ER LVEFGAP HAVKMDVYNL GDQTGVLLKA LAGVPVAHIE GTKYHLKSGH VTCEVGLEKL KMKGLTYTMC DKTKFTWKRA PTD SGHDTV VMEVTFSGTK PCRIPVRAVA HGSPDVNVAM LITPNPTIEN NGGGFIEMQL PPGDNIIYVG ELSHQWFQKG SSIG RVFQK TKKGIERLTV IGEHAWDFGS AGGFLSSIGK AVHTVLGGAF NSIFGGVGFL PKLLLGVALA WLGLNMRNPT MSMSF LLAG GLVLAMTLGV GA

UniProtKB: Genome polyprotein

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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
Source (natural)Organism: Tick-borne encephalitis virus (WESTERN SUBTYPE) / Strain: Neudoerfl
Molecular weightTheoretical: 8.311854 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SVLIPSHAQG ELTGRGHKWL EGDSLRTHLT RVEGWVWKNK LLALAMVTVV WLTLESVVTR VAVLVVLLCL APVYA

UniProtKB: Genome polyprotein

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Macromolecule #4: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 4 / Number of copies: 6 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 642026
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119210
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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