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- PDB-9uzf: Crystal structure of Kasokero virus cap- snatching endonuclease (... -

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Basic information

Entry
Database: PDB / ID: 9uzf
TitleCrystal structure of Kasokero virus cap- snatching endonuclease (D719A mutant)
Components
  • RNA-directed RNA polymerase L
  • mAb 2E9 Fab heavy chain
  • mAb 2E9 Fab light chain
KeywordsHYDROLASE / cap-snatching endonuclease
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 speciesMus musculus (house mouse)
Kasokero virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsDeng, Z. / Kuang, W. / Tian, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structure and function of the nairovirus cap-snatching endonuclease
Authors: Kuang, W. / Tian, Z. / Zhang, G. / Wu, F. / Li, J. / Tang, J. / Zhang, H. / Zhuo, X. / Hu, Z. / Wang, M. / Zhao, H. / Deng, Z.
History
DepositionMay 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,0053
Polymers83,0053
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.120, 81.150, 116.800
Angle α, β, γ (deg.)90.00, 97.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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) / Production host: Homo sapiens (human)
#2: 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) / Production host: Homo sapiens (human)
#3: Protein RNA-directed RNA polymerase L / Large structural protein / Replicase / Transcriptase


Mass: 34311.023 Da / Num. of mol.: 1 / Mutation: D719A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kasokero virus / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0M5KLS1, RNA-directed RNA polymerase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
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: 41.44 %
Crystal growTemperature: 298 K / Method: evaporation
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: BL02U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.47→29.33 Å / Num. obs: 24663 / % possible obs: 99.6 % / Redundancy: 3.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.09 / Rrim(I) all: 0.105 / Net I/σ(I): 7.5
Reflection shellResolution: 2.47→2.57 Å / Rmerge(I) obs: 0.658 / Num. unique obs: 2738 / CC1/2: 0.988 / Rpim(I) all: 0.569 / Rrim(I) all: 0.873 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→29.33 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1241 5.04 %
Rwork0.2001 --
obs0.2029 24637 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.47→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 0 115 5252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095256
X-RAY DIFFRACTIONf_angle_d1.1587139
X-RAY DIFFRACTIONf_dihedral_angle_d5.962721
X-RAY DIFFRACTIONf_chiral_restr0.065802
X-RAY DIFFRACTIONf_plane_restr0.011910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.570.33871380.28412544X-RAY DIFFRACTION100
2.57-2.690.33351210.28022628X-RAY DIFFRACTION100
2.69-2.830.33991430.25252601X-RAY DIFFRACTION100
2.83-30.29371440.2412564X-RAY DIFFRACTION100
3-3.240.30111680.22092579X-RAY DIFFRACTION100
3.24-3.560.2771470.20162583X-RAY DIFFRACTION99
3.56-4.080.24781020.18962639X-RAY DIFFRACTION99
4.08-5.130.20281410.15942596X-RAY DIFFRACTION100
5.13-29.330.19531370.1692662X-RAY DIFFRACTION99

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