9SWK | pdb_00009swk

Immature TBEV envelope spike with interaction partners underneath - SPA

  • Classification: VIRUS
  • Organism(s): Tick-borne encephalitis virus
  • Mutation(s): No 

  • Deposited: 2025-10-07 Released: 2026-05-20 
  • Deposition Author(s): Fuzik, T., Plevka, P., Smerdova, L., Nepovimova, L.
  • Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, European Research Council (ERC), Swedish Research Council, Academy of Finland, Sigrid Juselius Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9SWK

This is version 1.1 of the entry. See complete history

Literature

Structures of asymmetric particles of tick-borne encephalitis virus provide insight into flavivirus assembly and maturation.

Fuzik, T.Anastasina, M.Pajtinka, P.Domanska, A.Pulkkinen, L.I.A.Smerdova, L.Nepovimova, L.Formanova-Pokorna, P.Strakova, P.Novacek, J.Ruzek, D.Vacha, R.Butcher, S.J.Plevka, P.

(2026) Sci Adv 12: eaee4765-eaee4765

  • DOI: https://doi.org/10.1126/sciadv.aee4765
  • Primary Citation Related Structures: 
    9SWK

  • PubMed Abstract: 

    Flaviviruses are globally distributed human pathogens. However, the mechanisms underlying flavivirus assembly and maturation remain poorly understood. Here, we show that many particles of tick-borne encephalitis virus (TBEV) are asymmetric and lack subsets of surface heterodimers. Immature particles of TBEV contain incomplete spikes, providing evidence that their coats assemble directly from heterodimers of premembrane (prM) and envelope (E) proteins. Exposure of TBEV particles to acidic pH in the Golgi complex promotes maturation. The spikes and herringbone regions in TBEV maturation intermediates are oriented randomly rather than conforming to a common icosahedral symmetry. Consequently, the mature herringbone lattice forms around a randomly oriented nucleation center, expanding by addition of membrane-envelope heterodimers as the spikes disassemble and prMs are cleaved. The observed incompleteness of the protein coats explains, as an alternative to particle breathing, how flaviviruses can be neutralized by antibodies that bind to regions of E proteins normally inaccessible in the spiky or herringbone structures.


  • Organizational Affiliation
    • Central European Institute of Technology, Masaryk University, Brno, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 376.99 kDa 
  • Atom Count: 19,177 
  • Modeled Residue Count: 2,610 
  • Deposited Residue Count: 3,465 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope protein E
A, B, C, G, H
A, B, C, G, H, I
496Tick-borne encephalitis virusMutation(s): 0 
UniProt
Find proteins for P14336 (Tick-borne encephalitis virus European subtype (strain Neudoerfl))
Explore P14336 
Go to UniProtKB:  P14336
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14336
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein prM
D, E, F
163Tick-borne encephalitis virusMutation(s): 0 
UniProt
Find proteins for P14336 (Tick-borne encephalitis virus European subtype (strain Neudoerfl))
Explore P14336 
Go to UniProtKB:  P14336
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14336
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5.0
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLX22NPO5103
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2023050
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2023042
European Research Council (ERC)European Union101043452
Swedish Research CouncilSweden2018-05851
Academy of FinlandFinland315950
Sigrid Juselius FoundationFinland95-7202-38

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-20
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references