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- PDB-11ny: Crystal Structure of viral OTU domain protease from Tacheng Tick ... -

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Basic information

Entry
Database: PDB / ID: 11ny
TitleCrystal Structure of viral OTU domain protease from Tacheng Tick Virus 1
ComponentsRNA-directed RNA polymerase L
KeywordsHYDROLASE / TTV1 / L-protein / Viral OTU / deUbiquitinase / deISGlyase
Function / homology
Function and homology information


RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / membrane
Similarity search - Function
: / 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.
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesOrthonairovirus tachengense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsGonzalez, D.S. / Pegan, S.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI151006-S2 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI151006 United States
CitationJournal: Acs Infect Dis. / Year: 2026
Title: Insights into the Structure and Function of the OTU Protease Virulence Factors from Emerging Human Nairoviruses.
Authors: Gonzalez, D.S. / Jalf, A. / Moresco, V. / Garcia, J. / Jaroszewski, L. / Matta, D. / Nguyen, J. / Torres, B. / Bergeron, E. / Godzik, A. / Pegan, S.D.
History
DepositionMar 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0362
Polymers19,9401
Non-polymers961
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.767, 58.070, 59.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19940.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthonairovirus tachengense / Production host: Escherichia coli (E. coli) / Strain (production host): T7
References: UniProt: A0A0B5KXW6, RNA-directed RNA polymerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.69 Å3/Da / Density % sol: 27.2 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Lithium sullfate, 21 % PEG 3350, 0.1M Bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.366→29.63 Å / Num. obs: 35646 / % possible obs: 97.7 % / Redundancy: 5.9 % / CC1/2: 0.997 / Net I/σ(I): 1.778
Reflection shellResolution: 1.366→1.389 Å / Num. unique obs: 3392 / CC1/2: 0.284

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→29.63 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 1736 5 %
Rwork0.1613 --
obs0.1634 34708 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.37→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 5 235 1483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121320
X-RAY DIFFRACTIONf_angle_d1.2371810
X-RAY DIFFRACTIONf_dihedral_angle_d13.596476
X-RAY DIFFRACTIONf_chiral_restr0.109202
X-RAY DIFFRACTIONf_plane_restr0.01234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.410.39741130.332134X-RAY DIFFRACTION76
1.41-1.450.28881200.28962585X-RAY DIFFRACTION93
1.45-1.50.28881410.24442732X-RAY DIFFRACTION99
1.5-1.560.25411530.18672795X-RAY DIFFRACTION100
1.56-1.630.20891230.162801X-RAY DIFFRACTION100
1.63-1.720.1871620.14322795X-RAY DIFFRACTION100
1.72-1.830.17991460.14442805X-RAY DIFFRACTION100
1.83-1.970.21461720.14152779X-RAY DIFFRACTION100
1.97-2.170.17171540.13472823X-RAY DIFFRACTION100
2.17-2.480.19621380.15342850X-RAY DIFFRACTION100
2.48-3.130.20181370.17112892X-RAY DIFFRACTION100
3.13-29.630.18521770.14982981X-RAY DIFFRACTION100

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