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- EMDB-18614: Inactivated tick-borne encephalitis virus (TBEV) vaccine strain S... -

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Basic information

Entry
Database: EMDB / ID: EMD-18614
TitleInactivated tick-borne encephalitis virus (TBEV) vaccine strain Sofjin-Chumakov
Map dataLocal refinement of one virion shell raft after the symmetry expansion.
Sample
  • Virus: Tick-borne encephalitis virus (STRAIN Sofjin-Chumakov)
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Small envelope protein M
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTBEV / flavivirus / virion envelope / VIRAL PROTEIN
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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 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 / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor 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 ...: / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor 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. / 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, flavivirus / Flavivirus envelope glycoprotein M / 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
Envelope protein / Genome polyprotein
Similarity search - Component
Biological speciesOrthoflavivirus encephalitidis / Tick-borne encephalitis virus (STRAIN Sofjin-Chumakov)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMoiseenko AV / Zhang Y / Vorovitch M / Ivanova A / Liu Z / Osolodkin DI / Egorov A / Ishmukhametov A / Sokolova OS
Funding support Russian Federation, 2 items
OrganizationGrant numberCountry
Other government23A-Sh04-01
Ministry of Education and Science of the Russian FederationFNZG-2022-0002 Russian Federation
CitationJournal: Emerg Microbes Infect / Year: 2024
Title: The structure of inactivated mature tick-borne encephalitis virus at 3.0 Å resolution.
Authors: Evgeny B Pichkur / Mikhail F Vorovitch / Alla L Ivanova / Elena V Protopopova / Valery B Loktev / Dmitry I Osolodkin / Aydar A Ishmukhametov / Valeriya R Samygina /
Abstract: Tick-borne encephalitis virus (TBEV) causes a severe disease, tick-borne encephalitis (TBE), that has a substantial epidemiological importance for Northern Eurasia. Between 10,000 and 15,000 TBE ...Tick-borne encephalitis virus (TBEV) causes a severe disease, tick-borne encephalitis (TBE), that has a substantial epidemiological importance for Northern Eurasia. Between 10,000 and 15,000 TBE cases are registered annually despite the availability of effective formaldehyde-inactivated full-virion vaccines due to insufficient vaccination coverage, as well as sporadic cases of vaccine breakthrough. The development of improved vaccines would benefit from the atomic resolution structure of the antigen. Here we report the refined single-particle cryo-electron microscopy (cryo-EM) structure of the inactivated mature TBEV vaccine strain Sofjin-Chumakov (Far-Eastern subtype) at a resolution of 3.0 Å. The increase of the resolution with respect to the previously published structures of TBEV strains Hypr and Kuutsalo-14 (European subtype) was reached due to improvement of the virus sample quality achieved by the optimized preparation methods. All the surface epitopes of TBEV were structurally conserved in the inactivated virions. ELISA studies with monoclonal antibodies supported the hypothesis of TBEV protein shell cross-linking upon inactivation with formaldehyde.
History
DepositionOct 7, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18614.png

Downloads & links

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Map

FileDownload / File: emd_18614.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement of one virion shell raft after the symmetry expansion.
Voxel sizeX=Y=Z: 1.275 Å
Density
Contour LevelBy AUTHOR: 0.139
Minimum - Maximum-0.6935418 - 1.2334762
Average (Standard dev.)0.0029135214 (±0.037418135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 382.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: variability analysis class002 unsharpened map

Fileemd_18614_additional_1.map
Annotationvariability analysis class002 unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: variability analysis class001 unsharpened map

Fileemd_18614_additional_2.map
Annotationvariability analysis class001 unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: variability analysis class003 unsharpened map

Fileemd_18614_additional_3.map
Annotationvariability analysis class003 unsharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: variability analysis class000 unsharpened map

Fileemd_18614_additional_4.map
Annotationvariability analysis class000 unsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Full virion refinement with I symmetry

Fileemd_18614_additional_5.map
AnnotationFull virion refinement with I symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18614_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18614_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Tick-borne encephalitis virus (STRAIN Sofjin-Chumakov)

EntireName: Tick-borne encephalitis virus (STRAIN Sofjin-Chumakov)
Components
  • Virus: Tick-borne encephalitis virus (STRAIN Sofjin-Chumakov)
    • Protein or peptide: Genome polyprotein
    • 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 Sofjin-Chumakov)

SupramoleculeName: Tick-borne encephalitis virus (STRAIN Sofjin-Chumakov)
type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 11087
Sci species name: Tick-borne encephalitis virus (STRAIN Sofjin-Chumakov)
Sci species strain: Sofjin-Chumakov / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Details: KC806252.1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Orthoflavivirus encephalitidis / Strain: Sofjin-Chumakov
Molecular weightTheoretical: 53.43209 KDa
SequenceString: SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDSIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQSG TVCKRDQSDR GWGNHCGLFG KGSIVTCVKA SCEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS ...String:
SRCTHLENRD FVTGTQGTTR VTLVLELGGC VTITAEGKPS MDVWLDSIYQ ENPAKTREYC LHAKLSDTKV AARCPTMGPA TLAEEHQSG TVCKRDQSDR GWGNHCGLFG KGSIVTCVKA SCEAKKKATG HVYDANKIVY TVKVEPHTGD YVAANETHSG R KTASFTVS SEKTILTMGD YGDVSLLCRV ASGVDLAQTV ILELDKTSEH LPTAWQVHRD WFNDLALPWK HEGAQNWNNA ER LVEFGAP HAVKMDVYNL GDHTGVLLKS LAGVPVAHID GTKYHLKSGH VTCEVGLEKL KMKGLTYTMC DKTKFTWKRI PTD SGHDTV VMEVAFSGTK PCRIPVRAVA HGSPDVNVAM LITPNPIIEN NGGGFIEMQL PPGDNIIYVG ELSHQWFQKG SSIG RVFQK TRKGIERLTV IGEHAWDFGS AGGFLTSVGK ALHTVLGGAF NSLFGGVGFL PKILVGVVLA WLGLNMRNPT MSMSF LLAG GLVLAMTL

UniProtKB: Envelope protein

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Macromolecule #2: Small envelope protein M

MacromoleculeName: Small envelope protein M / type: protein_or_peptide / ID: 2 / Details: KC806252.1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Orthoflavivirus encephalitidis / Strain: Sofjin-Chumakov
Molecular weightTheoretical: 7.919407 KDa
SequenceString:
VLIPSHAQGE LTGRGHKWLE GDSLRTHLTR VEGWVWKNRL LALAMVTVVW LTLESVVTRV AVLVVLLCLA P

UniProtKB: Genome polyprotein

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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

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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: 7.8
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsDetails: The local non-uniform refinement was used on the set of particles subjected to icosahedral symmetry expansion
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5o6a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The local non-uniform refinement was used on the set of particles subjected to I symmetry expansion
Number images used: 70491
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5o6a


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8qrh:
Inactivated tick-borne encephalitis virus (TBEV) vaccine strain Sofjin-Chumakov

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