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- PDB-28ub: LASV cap-snatching endonuclease in complex with 2,4-dioxo-4-pheny... -

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Basic information

Entry
Database: PDB / ID: 28ub
TitleLASV cap-snatching endonuclease in complex with 2,4-dioxo-4-phenylbutanoic acid - serial synchrotron crystallography
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
2-4-DIOXO-4-PHENYLBUTANOIC ACID / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesMammarenavirus lassaense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 19, 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)23,2415
Polymers22,9221
Non-polymers3194
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-18 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.370, 58.370, 135.030
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

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Components

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


Mass: 22922.141 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-XI7 / 2-4-DIOXO-4-PHENYLBUTANOIC ACID


Mass: 192.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 293 K / Method: batch mode
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: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P09 HiPhaX / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.66→45.01 Å / Num. obs: 29030 / % possible obs: 100 % / Redundancy: 197.8 % / Biso Wilson estimate: 22.55 Å2 / CC1/2: 0.994 / CC star: 0.998 / Net I/σ(I): 8.3
Reflection shellResolution: 1.66→1.69 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1404 / CC1/2: 0.52 / CC star: 0.827

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Processing

Software
NameVersionClassification
PHENIX1.21.2-5419_9999refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→44.16 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2214 2000 7.05 %
Rwork0.2006 26388 -
obs0.2021 28388 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.95 Å2
Refinement stepCycle: LAST / Resolution: 1.66→44.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 20 80 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711450
X-RAY DIFFRACTIONf_angle_d0.82411963
X-RAY DIFFRACTIONf_chiral_restr0.0491223
X-RAY DIFFRACTIONf_plane_restr0.0056258
X-RAY DIFFRACTIONf_dihedral_angle_d12.9151561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.35691370.36841804X-RAY DIFFRACTION98.03
1.7-1.750.35011390.31971830X-RAY DIFFRACTION99.09
1.75-1.80.31321400.27911850X-RAY DIFFRACTION99.7
1.8-1.860.28931400.24211847X-RAY DIFFRACTION99.9
1.86-1.920.23361400.23411861X-RAY DIFFRACTION100
1.92-20.26841420.22291862X-RAY DIFFRACTION99.9
2-2.090.26471400.2291858X-RAY DIFFRACTION99.85
2.09-2.20.25931420.21781860X-RAY DIFFRACTION100
2.2-2.340.22051440.19321892X-RAY DIFFRACTION100
2.34-2.520.25611420.19181875X-RAY DIFFRACTION99.95
2.52-2.770.23621440.20381910X-RAY DIFFRACTION99.95
2.77-3.170.20511450.19551912X-RAY DIFFRACTION100
3.18-40.20371470.16591936X-RAY DIFFRACTION100
4-44.160.16921580.17962091X-RAY DIFFRACTION100

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