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 29IL | pdb_000029il

LASV cap-snatching endonuclease in complex with 2,4-dioxo-4-phenylbutanoic acid - SFX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.231 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Perspectives for pharmaceutical screening at XFEL sources using the example of Lassa virus endonuclease.

Falke, S., Reinke, P.Y.A., Rosenberg, D., Fischer, P., Meyer, J., Galchenkova, M., Tolstikova, A., Mariani, V., Senst, J.M., Lewe, P., Witt, S., Wagner, A., Chapman, H.N., Hunter, M., Gunther, S., Meents, A.

(2026) Acta Crystallogr D Struct Biol 

  • DOI: https://doi.org/10.1107/S2059798326009435
  • Primary Citation Related Structures: 
    28JG, 28JH, 28JI, 28UA, 28UB, 28UC, 29IK, 29IL, 29IM

  • PubMed Abstract: 

    Emerging human pathogenic RNA viruses such as Lassa virus (LASV) and closely related viruses such as Hantavirus and Andes virus continue to be a major health threat globally. Treatment options for infections are severely limited. The widely conserved cap-snatching endonuclease of LASV (LASVendoN) is therefore used as an interesting drug target for our X-ray compound-screening experiments. Considering recent improvements in instrumentation and serial crystallography method development, different approaches may be used to facilitate pharmaceutical compound screening. Current-generation X-ray free-electron laser (XFEL) sources hold promise for obtaining higher quality diffraction data and achieving a high sample throughput using fixed-target serial femtosecond X-ray crystallography. We collected serial fixed-target X-ray diffraction data at Linac Coherent Light Source and at the synchrotron source PETRA III for comparison and solved the crystal structures of 2,4-dioxo-4-phenylbutanoic acid (DPBA) and baloxavir acid (BXA) binding to the active site of LASVendoN. These solved structures represent a reasonable starting point for drug development. In addition to room-temperature diffraction data, conventional single-crystal diffraction data were recorded at 100 K for comparison. To analyse the sample throughput in a compound-screening experiment at an XFEL, we further present data for the bacterial fosfomycin-resistance protein A with six ligands previously identified in a synchrotron screening experiment. In summary, the XFEL and synchrotron data-collection approaches have proven to be useful for compound screening with minor differences in achievable data quality and resolution. The individual experimental setup, detector and potentially the use of beam sweeping at XFELs at close-to-physiological temperatures combined with reasonable sample consumption and minimized radiation damage are considered to be advantageous for high-throughput drug development.


  • Organizational Affiliation: 
    • Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 23.3 kDa 
  • Atom Count: 1,458 
  • Modeled Residue Count: 170 
  • Deposited Residue Count: 200 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L200Mammarenavirus lassaenseMutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for Q6GWS2 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976))
Explore Q6GWS2 
Go to UniProtKB:  Q6GWS2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GWS2
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.26α = 90
b = 58.26β = 90
c = 135.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Helmholtz AssociationGermanyFISCOV
Helmholtz AssociationGermanyFISVIR
Helmholtz AssociationGermanySFragX
Helmholtz AssociationGermanyInternLabs-0011-HIR3X
German Federal Ministry for Education and ResearchGermany13K22CHB
German Federal Ministry for Education and ResearchGermany16GW0277

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-07
    Type: Initial release