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- PDB-28ua: LASV cap-snatching endonuclease, serial synchrotron apo structure -

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Basic information

Entry
Database: PDB / ID: 28ua
TitleLASV cap-snatching endonuclease, serial synchrotron apo structure
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
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesMammarenavirus lassaense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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)22,9773
Polymers22,8901
Non-polymers862
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-3 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.630, 58.630, 135.640
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: 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.55 Å3/Da / Density % sol: 51.69 %
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: 1.81→45.21 Å / Num. obs: 22831 / % possible obs: 100 % / Redundancy: 99.7 % / Biso Wilson estimate: 24.41 Å2 / CC1/2: 0.989 / CC star: 0.997 / Net I/σ(I): 7
Reflection shellResolution: 1.81→1.86 Å / Num. unique obs: 1736 / CC1/2: 0.605 / CC star: 0.868

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Processing

Software
NameVersionClassification
PHENIX1.21.2-5419_9999refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→41.46 Å / SU ML: 0.1809 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1973
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2164 2000 8.94 %
Rwork0.1822 20363 -
obs0.1852 22363 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.57 Å2
Refinement stepCycle: LAST / Resolution: 1.81→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 5 80 1457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611487
X-RAY DIFFRACTIONf_angle_d0.70572026
X-RAY DIFFRACTIONf_chiral_restr0.0512234
X-RAY DIFFRACTIONf_plane_restr0.0056266
X-RAY DIFFRACTIONf_dihedral_angle_d13.2686577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.31591380.29581409X-RAY DIFFRACTION99.17
1.86-1.910.27761390.29331419X-RAY DIFFRACTION99.55
1.91-1.960.29141400.24051420X-RAY DIFFRACTION99.87
1.96-2.020.26281420.21841444X-RAY DIFFRACTION99.94
2.02-2.10.22891390.20381418X-RAY DIFFRACTION100
2.1-2.180.23341420.1921439X-RAY DIFFRACTION100
2.18-2.280.2021380.1881409X-RAY DIFFRACTION99.87
2.28-2.40.20721420.17481437X-RAY DIFFRACTION100
2.4-2.550.19361430.17491468X-RAY DIFFRACTION99.94
2.55-2.750.23831420.18261439X-RAY DIFFRACTION99.94
2.75-3.020.22271440.17761466X-RAY DIFFRACTION99.94
3.02-3.460.20181460.17661490X-RAY DIFFRACTION100
3.46-4.360.18281470.14441493X-RAY DIFFRACTION100
4.36-41.460.21481580.17561612X-RAY DIFFRACTION99.83

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