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- PDB-28jg: LASV cap-snatching endonuclease in complex with BXA - single crys... -

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Basic information

Entry
Database: PDB / ID: 28jg
TitleLASV cap-snatching endonuclease in complex with BXA - single crystal, cryo
ComponentsRNA-directed RNA polymerase L
KeywordsHYDROLASE / drug development / Lassa hemorrhagic fever / L protein / Arenaviridae
Function / homology
Function and homology information


negative stranded viral RNA replication / cap snatching / hydrolase activity / host cell / Hydrolases; Acting on ester bonds / nucleotide binding / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / host cell cytoplasm / metal ion binding
Similarity search - Function
RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Baloxavir acid / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesMammarenavirus lassaense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFalke, S. / Reinke, P.Y.A. / Senst, J.M. / Lewe, P. / Witt, S. / Meents, A. / Guenther, S.
Funding support Germany, 6items
OrganizationGrant numberCountry
Helmholtz AssociationFISCOV Germany
Helmholtz AssociationFISVIR Germany
Helmholtz AssociationSFragX Germany
Helmholtz AssociationInternLabs-0011-HIR3X Germany
German Federal Ministry for Education and Research13K22CHB Germany
German Federal Ministry for Education and Research16GW0277 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Perspectives for pharmaceutical screening at XFEL sources using the example of Lassa virus endonuclease.
Authors: 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. / ...Authors: 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.
History
DepositionFeb 3, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5765
Polymers22,8901
Non-polymers6864
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-22 kcal/mol
Surface area9830 Å2
Unit cell
Length a, b, c (Å)57.723, 57.723, 135.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-467-

HOH

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 22890.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus lassaense / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6GWS2, RNA-directed RNA polymerase, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-E4Z / Baloxavir acid


Mass: 483.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19F2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: After limited proteolysis with subtilisin A, 7.5 mg/ml target protein were mixed with an equal volume of crystallization solution (10% w/v PEG 10000, 250 mM MgSO4 and 100 mM Tris/HCl pH 9.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03322 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 17, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.75→53.08 Å / Num. obs: 23901 / % possible obs: 100 % / Redundancy: 26.3 % / Biso Wilson estimate: 27.88 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.155 / Net I/σ(I): 14.1
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1136 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
PHENIX2.0-5936_9999refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→53.08 Å / SU ML: 0.2827 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 1239 5.19 %RANDOM
Rwork0.226 22651 --
obs0.2275 23890 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.82 Å2
Refinement stepCycle: LAST / Resolution: 1.75→53.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 44 68 1472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01181454
X-RAY DIFFRACTIONf_angle_d1.24281970
X-RAY DIFFRACTIONf_chiral_restr0.0757224
X-RAY DIFFRACTIONf_plane_restr0.0112261
X-RAY DIFFRACTIONf_dihedral_angle_d14.4151586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.39071560.38452409X-RAY DIFFRACTION99.81
1.82-1.90.35571280.34162467X-RAY DIFFRACTION100
1.9-20.33651500.31262456X-RAY DIFFRACTION100
2-2.130.28721530.26162470X-RAY DIFFRACTION99.96
2.13-2.290.29751280.25112491X-RAY DIFFRACTION99.92
2.29-2.520.26751180.2262522X-RAY DIFFRACTION100
2.52-2.890.28881320.23552539X-RAY DIFFRACTION100
2.89-3.640.25481290.22432565X-RAY DIFFRACTION100
3.64-53.080.1931450.1812732X-RAY DIFFRACTION99.86

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