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- PDB-9uzb: Crystal structure of Kasokero virus cap-snatching endonuclease in... -

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Basic information

Entry
Database: PDB / ID: 9uzb
TitleCrystal structure of Kasokero virus cap-snatching endonuclease in apo form
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: 1.9 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


Theoretical massNumber of molelcules
Total (without water)82,6383
Polymers82,6383
Non-polymers00
Water12,863714
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)37.162, 80.906, 115.184
Angle α, β, γ (deg.)90.00, 93.47, 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: 33943.578 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
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: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→28.41 Å / Num. obs: 53558 / % possible obs: 99.5 % / Redundancy: 3.3 % / CC1/2: 0.972 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.128 / Rrim(I) all: 0.192 / Net I/σ(I): 6.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.451 / Num. unique obs: 3413 / CC1/2: 0.629 / Rpim(I) all: 0.412 / Rrim(I) all: 0.613 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.5 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2207 2766 5.18 %
Rwork0.1823 --
obs0.1842 53439 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5245 0 0 714 5959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085366
X-RAY DIFFRACTIONf_angle_d1.087279
X-RAY DIFFRACTIONf_dihedral_angle_d6.086726
X-RAY DIFFRACTIONf_chiral_restr0.067810
X-RAY DIFFRACTIONf_plane_restr0.009930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.27071440.22642549X-RAY DIFFRACTION99
1.93-1.970.25961240.21622538X-RAY DIFFRACTION100
1.97-2.010.24341410.20112489X-RAY DIFFRACTION100
2.01-2.050.26071440.20732553X-RAY DIFFRACTION100
2.05-2.090.23651520.20572485X-RAY DIFFRACTION100
2.09-2.140.25721370.19822541X-RAY DIFFRACTION100
2.14-2.190.28791240.19212572X-RAY DIFFRACTION100
2.19-2.250.22691390.19412491X-RAY DIFFRACTION100
2.25-2.320.21421370.19272561X-RAY DIFFRACTION100
2.32-2.390.22181330.19032503X-RAY DIFFRACTION100
2.39-2.480.21731660.19352521X-RAY DIFFRACTION99
2.48-2.580.22691380.19742492X-RAY DIFFRACTION100
2.58-2.70.26341370.19952567X-RAY DIFFRACTION100
2.7-2.840.25351380.20222527X-RAY DIFFRACTION100
2.84-3.020.26631410.18982516X-RAY DIFFRACTION100
3.02-3.250.2321350.18612564X-RAY DIFFRACTION100
3.25-3.570.19631510.16462520X-RAY DIFFRACTION99
3.57-4.090.15041370.15062564X-RAY DIFFRACTION99
4.09-5.150.16921140.13852564X-RAY DIFFRACTION99
5.15-27.50.19331340.17162556X-RAY DIFFRACTION97

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