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- PDB-9uom: Tacheng tick virus 1 nucleoprotein head domain -

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Basic information

Entry
Database: PDB / ID: 9uom
TitleTacheng tick virus 1 nucleoprotein head domain
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: 1.59 Å
AuthorsLi, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Tacheng tick virus 1 nucleoprotein
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)55,1636
Polymers54,7021
Non-polymers4605
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint1 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.260, 114.260, 54.863
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: 54702.199 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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 289.15 K / Method: liquid diffusion / 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: BL17U1 / Wavelength: 0.97853 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: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 55047 / % possible obs: 99.7 % / Redundancy: 19.7 % / CC1/2: 0.969 / Net I/σ(I): 11.8
Reflection shellResolution: 1.59→1.65 Å / Num. unique obs: 55047 / CC1/2: 0.969

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Processing

Software
NameVersionClassification
PHENIXv1refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.59→37.4 Å / SU ML: 0.1366 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.345
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1831 1984 3.64 %
Rwork0.1593 52580 -
obs0.1602 54564 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.68 Å2
Refinement stepCycle: LAST / Resolution: 1.59→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 30 452 3436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763066
X-RAY DIFFRACTIONf_angle_d0.95174155
X-RAY DIFFRACTIONf_chiral_restr0.057458
X-RAY DIFFRACTIONf_plane_restr0.0093522
X-RAY DIFFRACTIONf_dihedral_angle_d7.1786417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.22511360.18913612X-RAY DIFFRACTION95.81
1.63-1.670.21511370.17463740X-RAY DIFFRACTION99.28
1.67-1.720.19061400.16653727X-RAY DIFFRACTION99.36
1.72-1.780.18321390.16373764X-RAY DIFFRACTION99.34
1.78-1.840.1811460.15653739X-RAY DIFFRACTION99.41
1.84-1.920.18141450.1563753X-RAY DIFFRACTION99.54
1.92-20.18231380.15813787X-RAY DIFFRACTION99.64
2-2.110.17461370.16793755X-RAY DIFFRACTION99.62
2.11-2.240.18961440.15023748X-RAY DIFFRACTION99.31
2.24-2.410.17471420.15943747X-RAY DIFFRACTION99.13
2.41-2.660.21511460.16133751X-RAY DIFFRACTION99.01
2.66-3.040.20541430.16583792X-RAY DIFFRACTION99.57
3.04-3.830.16131450.14933796X-RAY DIFFRACTION99.34
3.83-37.40.16621460.15593869X-RAY DIFFRACTION99.04
Refinement TLS params.Method: refined / Origin x: 7.06516343233 Å / Origin y: 39.2182817015 Å / Origin z: 14.4504900525 Å
111213212223313233
T0.05441613002 Å20.00315656668601 Å20.0139775817781 Å2-0.0641181470298 Å20.0190123131158 Å2--0.0586340887264 Å2
L0.798924973085 °20.0116020596947 °20.0315588059983 °2-1.02164333576 °20.399633828322 °2--0.74345556563 °2
S-0.0161560003476 Å °0.00438772326146 Å °0.0362190642833 Å °0.0685522147864 Å °0.0226874590838 Å °0.0136110391956 Å °0.0144242566001 Å °-0.0195320060784 Å °-0.0128612262948 Å °
Refinement TLS groupSelection details: all

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