9FOJ

LGTV TP21. Langat virus, strain TP21

• PDB DOI: https://doi.org/10.2210/pdb9FOJ/pdb
• EM Map EMD-50624: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Langat virus (strain TP21)
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-06-12 Released: 2024-11-06 
• Deposition Author(s): Bisikalo, K., Rosendal, E.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

The influence of the pre-membrane and envelope proteins on structure, pathogenicity and tropism of tick-borne encephalitis virus

Rosendal, E., Bisikalo, K., Willekens, S.M., Lindgren, M., Holoubek, J., Svoboda, P., Lappalainen, A., Konighofer, E., Mirgorodskaya, E., Norden, R., Morini, F., Rosenbaum, W., Ruzek, D., Ahlgren, U., Anastasina, M., Merits, A., Butcher, S.J., Nilsson, E., Overby, A.K.

(2024) bioRxiv 

• DOI: https://doi.org/10.1101/2024.10.16.618642

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 360-mer - A180B180 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 191.29 kDa 
• Atom Count: 13,269 
• Modelled Residue Count: 1,710 
• Deposited Residue Count: 1,710 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	A, B, C	496	Langat virus (strain TP21)	Mutation(s): 0
UniProt
Find proteins for P29837 (Langat virus (strain TP21)) Explore P29837  Go to UniProtKB:  P29837
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small envelope protein M	D, E, F	74	Langat virus (strain TP21)	Mutation(s): 0
UniProt
Find proteins for P29837 (Langat virus (strain TP21)) Explore P29837  Go to UniProtKB:  P29837

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPL	J [auth A], K [auth A], L [auth B], M [auth B], N [auth C], O [auth C]	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C42 H80 N O8 P JLPULHDHAOZNQI-ZTIMHPMXSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	Coot

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Bisikalo, K., Rosendal, E.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2018-05851

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release
  
• Version 2.0: 2024-11-27
  Changes: Atomic model, Data collection, Derived calculations, Structure summary