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

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Basic information

Entry
Database: PDB / ID: 9uze
TitleCrystal structure of Kasokero virus cap- snatching endonuclease (E682A 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 speciesKasokero virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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
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)83,0464
Polymers82,9913
Non-polymers551
Water3,171176
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)37.176, 81.108, 115.871
Angle α, β, γ (deg.)90.00, 93.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34297.000 Da / Num. of mol.: 1 / Mutation: E682A
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
#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) / 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) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 289 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: 2.41→29.85 Å / Num. obs: 24612 / % possible obs: 92.4 % / Redundancy: 3.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.07 / Rrim(I) all: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 2.41→2.5 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2170 / CC1/2: 0.675 / Rpim(I) all: 0.394 / Rrim(I) all: 0.561 / % possible all: 78.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→29.85 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 1264 5.14 %
Rwork0.1782 --
obs0.181 24604 92.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5237 0 1 176 5414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085358
X-RAY DIFFRACTIONf_angle_d1.0117270
X-RAY DIFFRACTIONf_dihedral_angle_d6.178726
X-RAY DIFFRACTIONf_chiral_restr0.057811
X-RAY DIFFRACTIONf_plane_restr0.009928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.510.28411280.23932183X-RAY DIFFRACTION78
2.51-2.620.30791610.23092750X-RAY DIFFRACTION98
2.62-2.760.27811480.21972719X-RAY DIFFRACTION99
2.76-2.930.28441140.20632814X-RAY DIFFRACTION99
2.93-3.160.25981660.19832765X-RAY DIFFRACTION99
3.16-3.470.24181120.19082322X-RAY DIFFRACTION83
3.47-3.980.23151080.16772121X-RAY DIFFRACTION75
3.98-50.1991810.13782795X-RAY DIFFRACTION100
5.01-29.850.18381460.15582871X-RAY DIFFRACTION100

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