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- PDB-11ns: Crystal Structure of viral OTU domain protease from Pacific coast... -

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Basic information

Entry
Database: PDB / ID: 11ns
TitleCrystal Structure of viral OTU domain protease from Pacific coast tick nairovirus
ComponentsRNA-directed RNA polymerase L
KeywordsHYDROLASE / PCTN / 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
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. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
ACETATE ION / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesOrthonairovirus dermacentoris
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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
B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3366
Polymers44,9882
Non-polymers3474
Water5,044280
1
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6863
Polymers22,4941
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6493
Polymers22,4941
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.712, 70.712, 82.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 22494.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthonairovirus dermacentoris / Production host: Escherichia coli (E. coli) / Strain (production host): T7
References: UniProt: A0A2R2WU07, RNA-directed RNA polymerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.45 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.7 M Sodium Sulfate at pH 5.0, 0.37 M Sodium acetate, 0.15 mM CYMAL-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 55143 / % possible obs: 99.6 % / Redundancy: 7.3 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Rrim(I) all: 0.067 / Χ2: 1.112 / Net I/σ(I): 12.2 / Num. measured all: 403548
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.58-1.6170.33425630.9490.9870.1340.3610.54593
1.61-1.647.40.29227500.9640.9910.1140.3130.568100
1.64-1.677.40.2527430.970.9920.0980.2690.62100
1.67-1.77.40.23227530.9770.9940.0910.250.63999.9
1.7-1.747.30.20127540.9790.9950.080.2160.671100
1.74-1.787.20.17227750.9830.9960.0690.1860.781100
1.78-1.826.60.1527310.9850.9960.0630.1630.888100
1.82-1.877.70.13528120.9910.9980.0520.1440.992100
1.87-1.937.20.16527370.9830.9960.0680.1791.92100
1.93-1.997.60.11627640.9930.9980.0450.1241.404100
1.99-2.067.50.0927520.9950.9990.0350.0971.293100
2.06-2.147.20.08327780.9950.9990.0330.0891.557100
2.14-2.246.70.0827420.9950.9990.0330.0871.61100
2.24-2.367.30.07427940.9950.9990.030.081.546100
2.36-2.517.70.06827670.9960.9990.0260.0731.436100
2.51-2.77.60.06427730.9960.9990.0250.0681.265100
2.7-2.977.20.0627730.9970.9990.0240.0651.088100
2.97-3.47.80.05827730.9970.9990.0220.0621.18599.9
3.4-4.296.80.05627710.9970.9990.0230.0611.11299
4.29-507.60.05428380.9970.9990.0210.0581.07999.6

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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: 1.58→35.36 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 1996 3.63 %
Rwork0.1722 --
obs0.173 55026 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 19 280 2881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142737
X-RAY DIFFRACTIONf_angle_d1.3073738
X-RAY DIFFRACTIONf_dihedral_angle_d17.271963
X-RAY DIFFRACTIONf_chiral_restr0.092388
X-RAY DIFFRACTIONf_plane_restr0.01480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.23991330.21983702X-RAY DIFFRACTION97
1.62-1.670.23691450.19083789X-RAY DIFFRACTION100
1.67-1.720.22271450.18873753X-RAY DIFFRACTION100
1.72-1.770.2091440.18583766X-RAY DIFFRACTION100
1.77-1.830.2251430.17553772X-RAY DIFFRACTION100
1.83-1.910.21081420.18963821X-RAY DIFFRACTION100
1.91-20.26111460.20523741X-RAY DIFFRACTION99
2-2.10.17881470.18883792X-RAY DIFFRACTION100
2.1-2.230.23591450.16883804X-RAY DIFFRACTION100
2.23-2.40.17491370.17513804X-RAY DIFFRACTION100
2.4-2.650.26331460.18333808X-RAY DIFFRACTION100
2.65-3.030.21021450.18233805X-RAY DIFFRACTION100
3.03-3.810.14291440.16143804X-RAY DIFFRACTION100
3.82-35.360.18511340.1543869X-RAY DIFFRACTION99

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