8QRH

Inactivated tick-borne encephalitis virus (TBEV) vaccine strain Sofjin-Chumakov


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The structure of inactivated mature tick-borne encephalitis virus at 3.0 angstrom resolution.

Pichkur, E.B.Vorovitch, M.F.Ivanova, A.L.Protopopova, E.V.Loktev, V.B.Osolodkin, D.I.Ishmukhametov, A.A.Samygina, V.R.

(2024) Emerg Microbes Infect 13: 2313849-2313849

  • DOI: https://doi.org/10.1080/22221751.2024.2313849
  • Primary Citation of Related Structures:  
    8QRH, 8R8L

  • PubMed 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 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.


  • Organizational Affiliation

    NRC «Kurchatov Institute», Moscow, Russian Federation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein
A, B, C
492Orthoflavivirus encephalitidisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P07720 (Tick-borne encephalitis virus Far Eastern subtype (strain Sofjin))
Explore P07720 
Go to UniProtKB:  P07720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07720
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small envelope protein M
D, E, F
71Orthoflavivirus encephalitidisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H4LSY1 (Tick-borne encephalitis virus)
Explore A0A0H4LSY1 
Go to UniProtKB:  A0A0H4LSY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H4LSY1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government23A-Sh04-01
Ministry of Education and Science of the Russian FederationRussian FederationFNZG-2022-0002

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary