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- PDB-9xf9: Crystal structure of Kasokero virus cap- snatching endonuclease i... -

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Basic information

Entry
Database: PDB / ID: 9xf9
TitleCrystal structure of Kasokero virus cap- snatching endonuclease in complex with WXS
Components
  • RNA-directed RNA polymerase L
  • mAb 2E9 Fab heavy chain
  • mAb 2E9 Fab light chain
KeywordsHYDROLASE / cap-snatching endonuclease / inhibitor
Function / homology
Function and homology information


RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription
Similarity search - Function
: / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
: / : / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesKasokero virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDeng, Z. / Kuang, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2026
Title: Structures and inhibition of the Crimean-Congo haemorrhagic fever virus polymerase.
Authors: Lu Xue / Jiacheng Gui / Hainei Pan / Fan Wu / Shenghua Gao / Wenhua Kuang / Tiancai Chang / Zimu Li / Binqian Zou / Heyu Zhao / Mei Li / Min Zhou / Hongyu Yuan / Lijun Rong / Peng Gong / Jun ...Authors: Lu Xue / Jiacheng Gui / Hainei Pan / Fan Wu / Shenghua Gao / Wenhua Kuang / Tiancai Chang / Zimu Li / Binqian Zou / Heyu Zhao / Mei Li / Min Zhou / Hongyu Yuan / Lijun Rong / Peng Gong / Jun He / Zengqin Deng / Manli Wang / Peng Zhan / Xinwen Chen / Xiaoli Xiong /
Abstract: Crimean-Congo haemorrhagic fever virus (CCHFV) is a tick-borne virus and causes severe, often fatal, human infections. Lacking licensed vaccines or drugs, CCHFV is a World Health Organization ...Crimean-Congo haemorrhagic fever virus (CCHFV) is a tick-borne virus and causes severe, often fatal, human infections. Lacking licensed vaccines or drugs, CCHFV is a World Health Organization priority pathogen requiring urgent development of medical countermeasures. The CCHFV Large (L) protein functions as the viral RNA-dependent RNA polymerase CCHFV-L, representing a promising antiviral target, and is among the largest viral polymerases in the order Bunyavirales. Here we define the cofactors required for CCHFV-L RNA synthesis in vitro, enabling capture and determination of elongating CCHFV-L-RNA complex structures. The structures show a markedly enlarged polymerase architecture, revealing that CCHFV-L RNA synthesis is accompanied by ordering of the polymerase peripheral domains. We also define how the baloxavir-derived experimental drug WXSH0208 (ref. ) and the nucleoside analogue 2'-deoxy-2'-fluorocytidine, which has nanomolar cellular potency, inhibit this polymerase through endonuclease inhibition and post-translocation chain termination, respectively. Together, these results should structurally guide rational optimization of inhibitors directed against CCHFV-L.
History
DepositionOct 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 5, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
H: mAb 2E9 Fab heavy chain
L: mAb 2E9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5996
Polymers83,0503
Non-polymers5493
Water11,025612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.320, 80.600, 116.140
Angle α, β, γ (deg.)90.00, 93.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 34355.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kasokero virus / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: A0A0M5KLS1, RNA-directed RNA polymerase

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Antibody , 2 types, 2 molecules HL

#2: Antibody mAb 2E9 Fab heavy chain


Mass: 24722.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fab heavy chain / Production host: Homo sapiens (human)
#3: Antibody mAb 2E9 Fab light chain


Mass: 23971.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fab light chain / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 615 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1EZW / Cap-dependent endonuclease-IN-27


Mass: 439.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19F2N3O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25% vol/vol Jeffamine ED2003, 0.2 M NaCl, and 0.1 M MES-NaOH pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.85→28.99 Å / Num. obs: 57733 / % possible obs: 98.5 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3097 / CC1/2: 0.755 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→28.99 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 2894 5.01 %
Rwork0.1786 --
obs0.1804 57709 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 0 34 612 5892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085403
X-RAY DIFFRACTIONf_angle_d1.0427335
X-RAY DIFFRACTIONf_dihedral_angle_d6.868739
X-RAY DIFFRACTIONf_chiral_restr0.068813
X-RAY DIFFRACTIONf_plane_restr0.008936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.28141230.25032216X-RAY DIFFRACTION84
1.88-1.910.26081250.21512393X-RAY DIFFRACTION91
1.91-1.950.26211200.20392518X-RAY DIFFRACTION95
1.95-1.980.23021320.20022642X-RAY DIFFRACTION99
1.98-2.030.2381350.20082634X-RAY DIFFRACTION100
2.03-2.070.24621410.19092707X-RAY DIFFRACTION100
2.07-2.120.2371240.18992618X-RAY DIFFRACTION100
2.12-2.170.21441420.17812617X-RAY DIFFRACTION100
2.17-2.230.21691310.17522659X-RAY DIFFRACTION100
2.23-2.290.22411540.1812601X-RAY DIFFRACTION100
2.29-2.370.2111490.18042652X-RAY DIFFRACTION100
2.37-2.450.22161500.18662638X-RAY DIFFRACTION100
2.45-2.550.26211310.17962642X-RAY DIFFRACTION100
2.55-2.670.23091370.19292682X-RAY DIFFRACTION100
2.67-2.810.22491330.18462620X-RAY DIFFRACTION100
2.81-2.980.21911420.18072645X-RAY DIFFRACTION100
2.98-3.210.21981400.17482670X-RAY DIFFRACTION100
3.21-3.540.18481570.16912651X-RAY DIFFRACTION100
3.54-4.050.19521330.15832673X-RAY DIFFRACTION100
4.05-5.090.18031450.14962656X-RAY DIFFRACTION100
5.1-28.990.18291500.17612681X-RAY DIFFRACTION98

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