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- PDB-9x6q: Crystal structure of the Songling virus nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 9x6q
TitleCrystal structure of the Songling virus nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Orthonairovirus songlingense / viral nucleoprotein monomer
Function / homology: / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesOrthonairovirus songlingense
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsYanshin, A.O. / Gladysheva, A.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2025-452 Russian Federation
Citation
Journal: To Be Published
Title: Crystal structure of the Songling virus nucleoprotein
Authors: Yanshin, A.O. / Imatdinov, I.R. / Agafonov, A.P. / Gladysheva, A.V.
#1: Journal: Int J Mol Sci / Year: 2025
Title: Structural Features of Nucleoproteins from the Recently Discovered Orthonairovirus songlingense and Norwavirus beijiense.
Authors: Yanshin, A.O. / Ivkina, D.I. / Tuyrin, V.Y. / Osinkina, I.A. / Tishin, A.E. / Olkin, S.E. / Ukladov, E.O. / Radchenko, N.S. / Arkhipov, S.G. / Ryzhykau, Y.L. / Li, N. / Agafonov, A.P. / ...Authors: Yanshin, A.O. / Ivkina, D.I. / Tuyrin, V.Y. / Osinkina, I.A. / Tishin, A.E. / Olkin, S.E. / Ukladov, E.O. / Radchenko, N.S. / Arkhipov, S.G. / Ryzhykau, Y.L. / Li, N. / Agafonov, A.P. / Imatdinov, I.R. / Gladysheva, A.V.
History
DepositionOct 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7046
Polymers108,4172
Non-polymers2874
Water52229
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3152
Polymers54,2091
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21250 Å2
MethodPISA
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3894
Polymers54,2091
Non-polymers1813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.490, 113.352, 215.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-501-

PEG

21A-613-

HOH

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Components

#1: Protein Nucleoprotein


Mass: 54208.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthonairovirus songlingense / Plasmid: pET28b-14xHis / Production host: Escherichia coli KRX (bacteria)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 90 mM LiNaK (0.3 M Lithium sulfate, 0.3 M Sodium sulfate, 0.3 M Potassium sulfate); 0.1 M Buffer System 4 (1.0M MOPSO, Bis-Tris, PH 6.5); PH 6.5; 50 % v/v Precipitant Mix 6 (25% w/v PEG ...Details: 90 mM LiNaK (0.3 M Lithium sulfate, 0.3 M Sodium sulfate, 0.3 M Potassium sulfate); 0.1 M Buffer System 4 (1.0M MOPSO, Bis-Tris, PH 6.5); PH 6.5; 50 % v/v Precipitant Mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6- Hexanetriol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.52→56.68 Å / Num. obs: 45915 / % possible obs: 99.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 78.87 Å2 / CC1/2: 0.996 / Χ2: 0.91 / Net I/σ(I): 9.32
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 13 % / Num. unique obs: 4370 / CC1/2: 0.635 / Χ2: 0.52 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→34.27 Å / SU ML: 0.3945 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 35.2028 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2572 2346 5.12 %
Rwork0.2117 43442 -
obs0.2141 45788 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.73 Å2
Refinement stepCycle: LAST / Resolution: 2.52→34.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7541 0 16 29 7586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957732
X-RAY DIFFRACTIONf_angle_d1.108810428
X-RAY DIFFRACTIONf_chiral_restr0.05571113
X-RAY DIFFRACTIONf_plane_restr0.00611328
X-RAY DIFFRACTIONf_dihedral_angle_d25.81832845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.580.41611330.38492466X-RAY DIFFRACTION97.38
2.58-2.630.3851170.35482523X-RAY DIFFRACTION100
2.63-2.690.38231240.32462532X-RAY DIFFRACTION99.96
2.69-2.760.39761180.29642540X-RAY DIFFRACTION99.89
2.76-2.830.43321310.28892524X-RAY DIFFRACTION99.74
2.83-2.920.35841440.28222532X-RAY DIFFRACTION99.81
2.92-3.010.36711220.29422535X-RAY DIFFRACTION99.77
3.01-3.120.32541390.28042509X-RAY DIFFRACTION99.81
3.12-3.240.38481350.27652562X-RAY DIFFRACTION99.96
3.24-3.390.33071590.26762531X-RAY DIFFRACTION100
3.39-3.570.31741400.25322539X-RAY DIFFRACTION100
3.57-3.790.27231370.22312540X-RAY DIFFRACTION99.96
3.79-4.090.28831400.20222587X-RAY DIFFRACTION99.96
4.09-4.50.21961440.18032578X-RAY DIFFRACTION99.85
4.5-5.150.1961470.17322585X-RAY DIFFRACTION99.82
5.15-6.480.23011600.19482612X-RAY DIFFRACTION99.89
6.48-34.270.19261560.16142747X-RAY DIFFRACTION98.94

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