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- PDB-29il: LASV cap-snatching endonuclease in complex with 2,4-dioxo-4-pheny... -

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Basic information

Entry
Database: PDB / ID: 29il
TitleLASV cap-snatching endonuclease in complex with 2,4-dioxo-4-phenylbutanoic acid - SFX
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.02 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
DepositionMar 13, 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)23,3036
Polymers22,9221
Non-polymers3815
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-16 kcal/mol
Surface area9650 Å2
Unit cell
Length a, b, c (Å)58.260, 58.260, 135.380
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 32 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 50.91 %
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: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.265 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Oct 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.265 Å / Relative weight: 1
ReflectionResolution: 2.02→21.04 Å / Num. obs: 16532 / % possible obs: 100 % / Redundancy: 1380.6 % / Biso Wilson estimate: 39.53 Å2 / CC1/2: 0.984 / CC star: 0.996 / Net I/σ(I): 7.3
Reflection shellResolution: 2.02→2.05 Å / Num. unique obs: 779 / CC1/2: 0.858 / CC star: 0.961
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX2.0-5936_9999refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→20.6 Å / SU ML: 0.2363 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.103
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2305 1596 10 %
Rwork0.1903 14362 -
obs0.1942 15958 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.43 Å2
Refinement stepCycle: LAST / Resolution: 2.02→20.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 24 27 1425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731454
X-RAY DIFFRACTIONf_angle_d0.83121967
X-RAY DIFFRACTIONf_chiral_restr0.0477224
X-RAY DIFFRACTIONf_plane_restr0.0059258
X-RAY DIFFRACTIONf_dihedral_angle_d17.107562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.090.28761420.24271277X-RAY DIFFRACTION100
2.09-2.160.26021410.21931271X-RAY DIFFRACTION99.93
2.16-2.250.26271420.22411278X-RAY DIFFRACTION100
2.25-2.350.25981420.20651280X-RAY DIFFRACTION100
2.35-2.470.25881420.20751281X-RAY DIFFRACTION99.86
2.47-2.630.25051420.21611285X-RAY DIFFRACTION100
2.63-2.830.28541450.21451307X-RAY DIFFRACTION99.93
2.83-3.110.23981460.20011301X-RAY DIFFRACTION100
3.11-3.560.21541460.18271322X-RAY DIFFRACTION100
3.56-4.480.20841510.15291354X-RAY DIFFRACTION100
4.48-20.60.20331570.19081406X-RAY DIFFRACTION97.99

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