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 8WBH | pdb_00008wbh

CryoEM structure of non-structural protein 1 tetramer from Japanese encephalitis virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8WBH

This is version 1.2 of the entry. See complete history. 

Literature

The step-by-step assembly mechanism of secreted flavivirus NS1 tetramer and hexamer captured at atomic resolution.

Pan, Q., Jiao, H., Zhang, W., Chen, Q., Zhang, G., Yu, J., Zhao, W., Hu, H.

(2024) Sci Adv 10: eadm8275-eadm8275

  • DOI: https://doi.org/10.1126/sciadv.adm8275
  • Primary Citation Related Structures: 
    8WBB, 8WBC, 8WBD, 8WBE, 8WBF, 8WBG, 8WBH

  • PubMed Abstract: 

    Flaviviruses encode a conserved, membrane-associated nonstructural protein 1 (NS1) with replication and immune evasion functions. The current knowledge of secreted NS1 (sNS1) oligomers is based on several low-resolution structures, thus hindering the development of drugs and vaccines against flaviviruses. Here, we revealed that recombinant sNS1 from flaviviruses exists in a dynamic equilibrium of dimer-tetramer-hexamer states. Two DENV4 hexameric NS1 structures and several tetrameric NS1 structures from multiple flaviviruses were solved at atomic resolution by cryo-EM. The stacking of the tetrameric NS1 and hexameric NS1 is facilitated by the hydrophobic β-roll and connector domains. Additionally, a triacylglycerol molecule located within the central cavity may play a role in stabilizing the hexamer. Based on differentiated interactions between the dimeric NS1, two distinct hexamer models (head-to-head and side-to-side hexamer) and the step-by-step assembly mechanisms of NS1 dimer into hexamer were proposed. We believe that our study sheds light on the understanding of the NS1 oligomerization and contributes to NS1-based therapies.


  • Organizational Affiliation: 
    • Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong 518172, China.

Macromolecule Content 

  • Total Structure Weight: 163.58 kDa 
  • Atom Count: 10,284 
  • Modeled Residue Count: 1,293 
  • Deposited Residue Count: 1,432 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Genome polyproteinA,
B,
C [auth a],
D [auth b]
358Japanese encephalitis virusMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for Q82919 (Japanese encephalitis virus)
Explore Q82919 
Go to UniProtKB:  Q82919
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82919
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentJCYJ20210324131802008

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-06-25
    Changes: Data collection