7QRF

Structure of the dimeric complex between precursor membrane ectodomain (prM) and envelope protein ectodomain (E) from tick-borne encephalitis virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Evolution and activation mechanism of the flavivirus class II membrane-fusion machinery.

Vaney, M.C.Dellarole, M.Duquerroy, S.Medits, I.Tsouchnikas, G.Rouvinski, A.England, P.Stiasny, K.Heinz, F.X.Rey, F.A.

(2022) Nat Commun 13: 3718-3718

  • DOI: https://doi.org/10.1038/s41467-022-31111-y
  • Primary Citation of Related Structures:  
    7QRE, 7QRF, 7QRG

  • PubMed Abstract: 

    The flavivirus envelope glycoproteins prM and E drive the assembly of icosahedral, spiky immature particles that bud across the membrane of the endoplasmic reticulum. Maturation into infectious virions in the trans-Golgi network involves an acid-pH-driven rearrangement into smooth particles made of (prM/E) 2 dimers exposing a furin site for prM cleavage into "pr" and "M". Here we show that the prM "pr" moiety derives from an HSP40 cellular chaperonin. Furthermore, the X-ray structure of the tick-borne encephalitis virus (pr/E) 2 dimer at acidic pH reveals the E 150-loop as a hinged-lid that opens at low pH to expose a positively-charged pr-binding pocket at the E dimer interface, inducing (prM/E) 2 dimer formation to generate smooth particles in the Golgi. Furin cleavage is followed by lid-closure upon deprotonation in the neutral-pH extracellular environment, expelling pr while the 150-loop takes the relay in fusion loop protection, thus revealing the elusive flavivirus mechanism of fusion activation.


  • Organizational Affiliation

    Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein E443Tick-borne encephalitis virus (WESTERN SUBTYPE)Mutation(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
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptideB [auth C]5Tick-borne encephalitis virus (WESTERN SUBTYPE)Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyproteinC [auth D]138Tick-borne encephalitis virus (WESTERN SUBTYPE)Mutation(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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download Ideal Coordinates CCD File 
E [auth A]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth D],
M [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.73α = 90
b = 155.73β = 90
c = 161.88γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Pasteur InstituteFrance--
Centre National de la Recherche Scientifique (CNRS)France--
Agence Nationale de la Recherche (ANR)FranceANR-13-ISV8-0002-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary