8ZHZ | pdb_00008zhz

Structure of Ikoma lyssavirus glycoprotein in pre-fusion state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 
    0.281 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structures of two lyssavirus glycoproteins trapped in pre- and post-fusion states and the implications on the spatial-temporal conformational transition along with pH-decrease.

Yang, F.Lin, S.Yuan, X.Shu, S.Yu, Y.Yang, J.Ye, F.Chen, Z.He, B.Li, J.Zhao, Q.Ye, H.Cao, Y.Lu, G.

(2025) PLoS Pathog 21: e1012923-e1012923

  • DOI: https://doi.org/10.1371/journal.ppat.1012923
  • Primary Citation Related Structures: 
    8ZHW, 8ZHZ

  • PubMed Abstract: 

    Lyssavirus glycoprotein plays a crucial role in mediating virus entry and serves as the major target for neutralizing antibodies. During membrane fusion, the lyssavirus glycoprotein undergoes a series of low-pH-induced conformational transitions. Here, we report the structures of Ikoma lyssavirus and Mokola lyssavirus glycoproteins, with which we believe that we have trapped the proteins in pre-fusion and post-fusion states respectively. By analyzing the available lyssaviral glycoprotein structures, we present a sequential conformation-transition model, in which two structural elements in the glycoprotein undergo fine-modulated secondary structural transitions, changing the glycoprotein from a bended hairpin conformation to an extended linear conformation. In addition, such conformational change is further facilitated, as observed in our surface plasmon resonance assay, by the pH-regulated interactions between the membrane-proximal region and the pleckstrin homology and the fusion domains. The structural features elucidated in this study will facilitate the design of vaccines and anti-viral drugs against lyssaviruses.


  • Organizational Affiliation
    • Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.

Macromolecule Content 

  • Total Structure Weight: 303.05 kDa 
  • Atom Count: 17,908 
  • Modeled Residue Count: 2,204 
  • Deposited Residue Count: 2,640 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein
A, B, C, D, E
A, B, C, D, E, F
440Ikoma lyssavirusMutation(s): 0 
UniProt
Find proteins for J7JVS8 (Ikoma lyssavirus)
Explore J7JVS8 
Go to UniProtKB:  J7JVS8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7JVS8
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free:  0.281 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.915α = 90
b = 90.746β = 90.08
c = 151.311γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Database references