9SWK | pdb_00009swk

Immature TBEV envelope spike with interaction partners underneath - SPA

• PDB DOI: https://doi.org/10.2210/pdb9SWK/pdb
• EM Map EMD-55311: EMDB EMDataResource

• 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

Literature

Structures of asymmetric particles of TBEV 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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - C3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	A, B, C, G, H, I	496	Tick-borne encephalitis virus	Mutation(s): 0
UniProt
Find proteins for P14336 (Tick-borne encephalitis virus European subtype (strain Neudoerfl)) Explore P14336  Go to UniProtKB:  P14336
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein prM	D, E, F	163	Tick-borne encephalitis virus	Mutation(s): 0
UniProt
Find proteins for P14336 (Tick-borne encephalitis virus European subtype (strain Neudoerfl)) Explore P14336  Go to UniProtKB:  P14336

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth B], L [auth C], M [auth G], N [auth H], O [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5.0
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-20 
Deposition Author(s): Fuzik, T., Plevka, P., Smerdova, L., Nepovimova, L.

---

Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LX22NPO5103
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2023050
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2023042
European Research Council (ERC)	European Union	101043452
Swedish Research Council	Sweden	2018-05851
Academy of Finland	Finland	315950
Sigrid Juselius Foundation	Finland	95-7202-38

Revision History  

• Version 1.0: 2026-05-20
  Type: Initial release