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- PDB-11pu: Crystal Structure of viral OTU domain protease from Beiji nairovirus -

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Basic information

Entry
Database: PDB / ID: 11pu
TitleCrystal Structure of viral OTU domain protease from Beiji nairovirus
ComponentsRNA-directed RNA polymerase L
KeywordsHYDROLASE / BJNV / L protein / norwavirus / virulance factor
Function / homologyRNA-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. / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA-directed RNA polymerase L
Function and homology information
Biological speciesNorwavirus beijiense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI151006-S2 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 9, 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
C: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)41,5532
Polymers41,5532
Non-polymers00
Water5,927329
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-8 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.250, 73.629, 103.230
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: 20776.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwavirus beijiense / Production host: Escherichia coli (E. coli) / Strain (production host): T7
References: UniProt: A0AAX2ZL03, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES at pH 5.9, 1.2 M Sodium malonate, 30% w/v D-Sorbitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 56767 / % possible obs: 98.5 % / Redundancy: 7.3 % / CC1/2: 0.973 / CC star: 0.993 / Rrim(I) all: 0.752 / Net I/σ(I): 24.5
Reflection shellResolution: 1.5→4.07 Å / Num. unique obs: 16205 / CC1/2: 0.86 / CC star: 0.962 / Rpim(I) all: 0.279 / Χ2: 0.546

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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: 1.5→34.68 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 1997 3.53 %
Rwork0.1961 --
obs0.1975 56630 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→34.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2682 0 0 329 3011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142907
X-RAY DIFFRACTIONf_angle_d1.393984
X-RAY DIFFRACTIONf_dihedral_angle_d19.0021096
X-RAY DIFFRACTIONf_chiral_restr0.111463
X-RAY DIFFRACTIONf_plane_restr0.012512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.3091330.24113634X-RAY DIFFRACTION93
1.53-1.570.27741400.21413808X-RAY DIFFRACTION97
1.57-1.620.26761400.2073846X-RAY DIFFRACTION98
1.62-1.670.32411410.19743878X-RAY DIFFRACTION98
1.67-1.730.2771430.18753867X-RAY DIFFRACTION99
1.73-1.80.23931410.19673879X-RAY DIFFRACTION98
1.8-1.880.25581410.20063853X-RAY DIFFRACTION98
1.88-1.980.27411450.19013941X-RAY DIFFRACTION99
1.98-2.110.26061430.18223911X-RAY DIFFRACTION99
2.11-2.270.21091430.18583931X-RAY DIFFRACTION99
2.27-2.50.25321450.17973954X-RAY DIFFRACTION99
2.5-2.860.21341470.20033993X-RAY DIFFRACTION100
2.86-3.60.25641460.19884000X-RAY DIFFRACTION98
3.6-34.680.21731490.20024138X-RAY DIFFRACTION98

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