9FIZ

Structure of the F13 protein (mutant A295E) of Vaccinia virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.259 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CITClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


Literature

Structural insights into tecovirimat antiviral activity and poxvirus resistance.

Vernuccio, R.Martinez Leon, A.Poojari, C.S.Buchrieser, J.Selverian, C.N.Jaleta, Y.Meola, A.Guivel-Benhassine, F.Porrot, F.Haouz, A.Chevreuil, M.Raynal, B.Mercer, J.Simon-Loriere, E.Chandran, K.Schwartz, O.Hub, J.S.Guardado-Calvo, P.

(2025) Nat Microbiol 

  • DOI: https://doi.org/10.1038/s41564-025-01936-6
  • Primary Citation of Related Structures:  
    9FHK, 9FHS, 9FIZ, 9FJ0, 9FJ1, 9FJA, 9HAH

  • PubMed Abstract: 

    Mpox is a zoonotic disease endemic to Central and West Africa. Since 2022, two human-adapted monkeypox virus (MPXV) strains have caused large outbreaks outside these regions. Tecovirimat is the most widely used drug to treat mpox. It blocks viral egress by targeting the viral phospholipase F13; however, the structural details are unknown, and mutations in the F13 gene can result in resistance against tecovirimat, raising public health concerns. Here we report the structure of an F13 homodimer using X-ray crystallography, both alone (2.1 Å) and in complex with tecovirimat (2.6 Å). Combined with molecular dynamics simulations and dimerization assays, we show that tecovirimat acts as a molecular glue that promotes dimerization of the phospholipase. Tecovirimat resistance mutations identified in clinical MPXV isolates map to the F13 dimer interface and prevent drug-induced dimerization in solution and in cells. These findings explain how tecovirimat works, allow for better monitoring of resistant MPXV strains and pave the way for developing more potent and resilient therapeutics.


  • Organizational Affiliation

    G5 Structural Biology of Infectious Diseases, Institut Pasteur, Université Paris Cité, Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope phospholipase OPG057378Vaccinia virus Western ReserveMutation(s): 1 
Gene Names: OPG057VACWR052F13L
EC: 3.1.1 (PDB Primary Data), 3.1.4.4 (PDB Primary Data)
UniProt
Find proteins for P04021 (Vaccinia virus (strain Western Reserve))
Explore P04021 
Go to UniProtKB:  P04021
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04021
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT (Subject of Investigation/LOI)
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.259 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 280.979α = 90
b = 280.979β = 90
c = 280.979γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CITClick on this verticalbar to view detailsBest fitted GOLClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-22-CE11-0003

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release