7PLR

Crystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound Baloxavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biophysical and structural study of La Crosse virus endonuclease inhibition for the development of new antiviral options.

Feracci, M.Hernandez, S.Garlatti, L.Mondielli, C.Vincentelli, R.Canard, B.Reguera, J.Ferron, F.Alvarez, K.

(2024) IUCrJ 11: 374-383

  • DOI: https://doi.org/10.1107/S205225252400304X
  • Primary Citation of Related Structures:  
    7OA4, 7PLR

  • PubMed Abstract: 

    The large Bunyavirales order includes several families of viruses with a segmented ambisense (-) RNA genome and a cytoplasmic life cycle that starts by synthesizing viral mRNA. The initiation of transcription, which is common to all members, relies on an endonuclease activity that is responsible for cap-snatching. In La Crosse virus, an orthobunyavirus, it has previously been shown that the cap-snatching endonuclease resides in the N-terminal domain of the L protein. Orthobunyaviruses are transmitted by arthropods and cause diseases in cattle. However, California encephalitis virus, La Crosse virus and Jamestown Canyon virus are North American species that can cause encephalitis in humans. No vaccines or antiviral drugs are available. In this study, three known Influenza virus endonuclease inhibitors (DPBA, L-742,001 and baloxavir) were repurposed on the La Crosse virus endonuclease. Their inhibition was evaluated by fluorescence resonance energy transfer and their mode of binding was then assessed by differential scanning fluorimetry and microscale thermophoresis. Finally, two crystallographic structures were obtained in complex with L-742,001 and baloxavir, providing access to the structural determinants of inhibition and offering key information for the further development of Bunyavirales endonuclease inhibitors.


  • Organizational Affiliation

    Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB)-UMR7257 CNRS-Case 932, 163 Avenue de Luminy, 13288 Marseille CEDEX 09, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase LA [auth AAA],
B [auth BBB],
C [auth DDD],
D [auth GGG]
184La Crosse virusMutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for A5HC98 (Bunyavirus La Crosse)
Explore A5HC98 
Go to UniProtKB:  A5HC98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5HC98
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E4Z (Subject of Investigation/LOI)
Query on E4Z

Download Ideal Coordinates CCD File 
E [auth AAA],
O [auth DDD],
S [auth GGG]
Baloxavir acid
C24 H19 F2 N3 O4 S
FIDLLEYNNRGVFR-CTNGQTDRSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth AAA]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
I [auth AAA]
J [auth AAA]
K [auth AAA]
L [auth BBB]
M [auth BBB]
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth BBB],
M [auth BBB],
N [auth BBB],
Q [auth DDD],
R [auth DDD],
U [auth GGG],
V [auth GGG]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
F [auth AAA],
H [auth AAA],
P [auth DDD],
T [auth GGG]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.738α = 90
b = 124.738β = 90
c = 295.25γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-18-ASTR-0010-01, PaNuVi

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-09-18
    Changes: Database references