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

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Basic information

Entry
Database: PDB / ID: 9uzd
TitleCrystal structure of Kasokero virus cap- snatching endonuclease (E668A 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: 2.4 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
Water2,450136
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)37.189, 80.332, 116.262
Angle α, β, γ (deg.)90.00, 97.74, 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: E668A
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.: 136 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
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: 2.4→29.3 Å / Num. obs: 25265 / % possible obs: 94.9 % / Redundancy: 4.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.068 / Rrim(I) all: 0.111 / Net I/σ(I): 9.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.516 / Num. unique obs: 2229 / CC1/2: 0.652 / Rpim(I) all: 0.424 / Rrim(I) all: 0.672 / % possible all: 79.1

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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: 2.4→29.3 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1226 4.86 %
Rwork0.1905 --
obs0.1932 25245 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 1 136 5239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085220
X-RAY DIFFRACTIONf_angle_d1.1367099
X-RAY DIFFRACTIONf_dihedral_angle_d6.014722
X-RAY DIFFRACTIONf_chiral_restr0.062803
X-RAY DIFFRACTIONf_plane_restr0.01907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.32391080.25152271X-RAY DIFFRACTION80
2.5-2.610.32521420.25972693X-RAY DIFFRACTION97
2.61-2.750.33231440.23092709X-RAY DIFFRACTION98
2.75-2.920.27221380.21732757X-RAY DIFFRACTION98
2.92-3.140.24821540.20972782X-RAY DIFFRACTION99
3.14-3.460.3061240.19912327X-RAY DIFFRACTION83
3.46-3.960.25521310.17762804X-RAY DIFFRACTION99
3.96-4.980.20471500.15592806X-RAY DIFFRACTION99
4.99-29.30.18891350.17352870X-RAY DIFFRACTION99

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