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- PDB-9uon: Tacheng tick virus 1 nucleoprotein head domain with selenomethionine -

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Basic information

Entry
Database: PDB / ID: 9uon
TitleTacheng tick virus 1 nucleoprotein head domain with selenomethionine
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Nairovirus / nucleoprotein
Function / homologyNucleocapsid N protein / Nucleocapsid N protein / helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / RNA binding / Nucleoprotein
Function and homology information
Biological speciesTacheng Tick Virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsLi, Z. / Litao, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Tacheng tick virus 1 nucleoprotein head domain with selenomethionine
Authors: Li, Z.
History
DepositionApr 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9117
Polymers55,3591
Non-polymers5536
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint1 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.166, 113.166, 54.117
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 55358.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tacheng Tick Virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C0C9F4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M LiSO4,20%PEG 3350,

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 103756 / % possible obs: 100 % / Redundancy: 19.9 % / CC1/2: 0.969 / Net I/σ(I): 11.8
Reflection shellResolution: 1.55→1.61 Å / Num. unique obs: 57834 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→37.04 Å / SU ML: 0.1505 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.703
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1987 3907 3.77 %
Rwork0.1688 99849 -
obs0.17 103756 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.53 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 36 462 3468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01053082
X-RAY DIFFRACTIONf_angle_d1.14244171
X-RAY DIFFRACTIONf_chiral_restr0.0648458
X-RAY DIFFRACTIONf_plane_restr0.0106523
X-RAY DIFFRACTIONf_dihedral_angle_d7.425418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.3413750.29292023X-RAY DIFFRACTION52.28
1.57-1.590.3091890.26982320X-RAY DIFFRACTION60.19
1.59-1.610.2856940.25362581X-RAY DIFFRACTION66.36
1.61-1.630.3332990.2512759X-RAY DIFFRACTION71.97
1.63-1.660.27511240.22982948X-RAY DIFFRACTION76.63
1.66-1.680.27151260.2343121X-RAY DIFFRACTION81.13
1.68-1.710.22431300.22333409X-RAY DIFFRACTION87.88
1.71-1.730.25761360.2153562X-RAY DIFFRACTION92.13
1.73-1.760.24381480.21733745X-RAY DIFFRACTION96.24
1.76-1.80.23741410.20743861X-RAY DIFFRACTION99.16
1.8-1.830.22571460.20453849X-RAY DIFFRACTION99.78
1.83-1.870.23521530.19533889X-RAY DIFFRACTION99.78
1.87-1.910.21181540.19323830X-RAY DIFFRACTION99.85
1.91-1.950.22791460.17033876X-RAY DIFFRACTION99.95
1.95-20.19611560.16763869X-RAY DIFFRACTION99.98
2-2.060.21391560.1643876X-RAY DIFFRACTION100
2.06-2.120.17211520.15853828X-RAY DIFFRACTION100
2.12-2.180.17811480.15313865X-RAY DIFFRACTION100
2.18-2.260.18731560.16163889X-RAY DIFFRACTION100
2.26-2.350.18831540.15373877X-RAY DIFFRACTION100
2.35-2.460.20851540.15183862X-RAY DIFFRACTION100
2.46-2.590.20731520.16543821X-RAY DIFFRACTION100
2.59-2.750.191570.16283854X-RAY DIFFRACTION100
2.75-2.960.20091580.16373883X-RAY DIFFRACTION100
2.97-3.260.20011520.15043857X-RAY DIFFRACTION100
3.26-3.730.15751590.14533887X-RAY DIFFRACTION100
3.74-4.70.17451460.1323848X-RAY DIFFRACTION99.97
4.7-37.040.15741460.17023860X-RAY DIFFRACTION99.33
Refinement TLS params.Method: refined / Origin x: 7.36378710711 Å / Origin y: 38.5233315071 Å / Origin z: 14.132780574 Å
111213212223313233
T0.0743638214078 Å20.00273245779 Å20.00253246508867 Å2-0.0705242496842 Å20.0250819106104 Å2--0.0735291224556 Å2
L0.812406009257 °20.0200293125744 °20.00291183392901 °2-1.21618185739 °20.402544073059 °2--0.74675042307 °2
S-0.00689414695892 Å °0.00630330839209 Å °0.0492986341607 Å °0.0945343032006 Å °0.0113084194295 Å °0.00510619281925 Å °0.0144987655213 Å °-0.0199407017206 Å °-0.00638179228763 Å °
Refinement TLS groupSelection details: all

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