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- EMDB-19003: The structure of inactivated mature tick-borne encephalitis virus -
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Open data
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Basic information
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Title | The structure of inactivated mature tick-borne encephalitis virus | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Pichkur EB / Samygina VR | |||||||||
Funding support | 1 items
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 39.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.3 KB 14.3 KB | Display Display | ![]() |
Images | ![]() | 306.2 KB | ||
Masks | ![]() | 600.7 MB | ![]() | |
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 555.1 MB 555.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8r8lMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.2785 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
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Sample components
-Entire : Tick-borne encephalitis virus (STRAIN SOFJIN)
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Tick-borne encephalitis virus (STRAIN SOFJIN)
Supramolecule | Name: Tick-borne encephalitis virus (STRAIN SOFJIN) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 11087 Sci species name: Tick-borne encephalitis virus (STRAIN SOFJIN) Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: Peptide 2k
Macromolecule | Name: Peptide 2k / type: protein_or_peptide / ID: 1 Details: TGTQG loop was deleted, as there is no EM-density to support it's modelling Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.376238 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 UniProtKB: Genome polyprotein |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 66.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: I (icosahedral![]() |