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- PDB-11nq: Crystal structure of viral OTU domain protease from Songling Virus -

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Basic information

Entry
Database: PDB / ID: 11nq
TitleCrystal structure of viral OTU domain protease from Songling Virus
ComponentsRNA-directed RNA polymerase L
KeywordsHYDROLASE / SGLV / 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.
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesOrthonairovirus songlingense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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)R01Al151006-S2 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01Al151006 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)21,3004
Polymers21,0291
Non-polymers2713
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: ASU was confirmed via Xtriage in Phenix
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.765, 52.674, 61.985
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: 21028.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthonairovirus songlingense / Production host: Escherichia coli (E. coli) / Strain (production host): T7
References: UniProt: A0A7U3T2V7, RNA-directed RNA polymerase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 260 / 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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium acetate, 18% PEGs 3350, 0.1M Yttrium (III) chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 47281 / % possible obs: 96.2 % / Redundancy: 3.6 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.022 / Rrim(I) all: 0.06 / Χ2: 0.816 / Net I/σ(I): 8.5 / Num. measured all: 323105
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.22-1.242.40.22517350.960.990.1150.2540.53271.9
1.24-1.262.50.20619670.9650.9910.1010.2310.55581.2
1.26-1.292.80.19222820.9720.9930.090.2130.5393.5
1.29-1.313.50.18223430.9850.9960.0750.1970.57497
1.31-1.343.60.16423560.9870.9970.0660.1770.57197
1.34-1.373.60.14823460.9890.9970.060.160.59797.8
1.37-1.413.70.1323800.9920.9980.0520.140.54897.9
1.41-1.453.50.11624040.9910.9980.0470.1260.57398.1
1.45-1.493.80.09823760.9940.9990.0380.1060.59798.3
1.49-1.543.90.08624090.9960.9990.0330.0920.59798.2
1.54-1.593.80.07724060.9970.9990.030.0830.64198.5
1.59-1.663.80.0723920.9970.9990.0280.0750.6898.3
1.66-1.733.60.06324350.9970.9990.0250.0680.68498.9
1.73-1.823.90.0624260.9970.9990.0230.0640.75499.3
1.82-1.943.90.05624460.9980.9990.0220.060.85699
1.94-2.093.80.05224470.9980.9990.0210.0561.01599.5
2.09-2.33.70.04724620.9980.9990.0190.0511.13799.3
2.3-2.6340.04524950.99810.0180.0491.2399.8
2.63-3.313.70.04225260.9980.9990.0170.0461.38399.6
3.31-503.90.04526480.9970.9990.0180.0491.73499.4

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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: 1.22→31.24 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1631 2008 4.25 %
Rwork0.1294 --
obs0.1308 47204 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→31.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1399 0 18 260 1677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121515
X-RAY DIFFRACTIONf_angle_d1.3242061
X-RAY DIFFRACTIONf_dihedral_angle_d14.374553
X-RAY DIFFRACTIONf_chiral_restr0.1223
X-RAY DIFFRACTIONf_plane_restr0.01269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.16651040.12172428X-RAY DIFFRACTION73
1.25-1.280.16321380.12192945X-RAY DIFFRACTION89
1.28-1.320.16571480.12463202X-RAY DIFFRACTION97
1.32-1.370.15681370.11293223X-RAY DIFFRACTION97
1.37-1.410.16021470.10263251X-RAY DIFFRACTION98
1.41-1.470.13441390.09943265X-RAY DIFFRACTION98
1.47-1.540.12511490.10063282X-RAY DIFFRACTION98
1.54-1.620.13081400.10093271X-RAY DIFFRACTION98
1.62-1.720.15521500.10813310X-RAY DIFFRACTION99
1.72-1.850.15541530.1173318X-RAY DIFFRACTION99
1.85-2.040.17031450.12443346X-RAY DIFFRACTION99
2.04-2.330.16081490.12513379X-RAY DIFFRACTION99
2.34-2.940.17441510.15543423X-RAY DIFFRACTION100
2.94-31.240.18261580.15473553X-RAY DIFFRACTION99

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