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- PDB-9up8: Tacheng tick virus 1 nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 9up8
TitleTacheng tick virus 1 nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Nairovirus / Tacheng tick virus 1 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsLi, Z. / Sun, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Tacheng tick virus 1 nucleoprotein
Authors: Li, Z. / Sun, L.
History
DepositionApr 27, 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
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)109,4042
Polymers109,4042
Non-polymers00
Water00
1
A: Nucleoprotein

A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)109,4042
Polymers109,4042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area4550 Å2
ΔGint-24 kcal/mol
Surface area38610 Å2
MethodPISA
2
B: Nucleoprotein

B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)109,4042
Polymers109,4042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3570 Å2
ΔGint-23 kcal/mol
Surface area39490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.557, 78.747, 92.636
Angle α, β, γ (deg.)90.000, 107.599, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 2 through 299 or resid 301 through 486))
d_2ens_1(chain "B" and (resid 2 through 181 or resid 195 through 486))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAGLYGLYAA2 - 2992 - 299
d_12PHEPHETYRTYRAA301 - 486301 - 486
d_21ALAALAALAALABB2 - 1812 - 181
d_22HISHISTYRTYRBB195 - 486195 - 486

NCS oper: (Code: givenMatrix: (-0.978913479386, -0.147734662348, 0.14107752981), (-0.142616603126, 0.988718657719, 0.0457812231264), (-0.146249459449, 0.0246958583422, -0.98893943707)Vector: 96. ...NCS oper: (Code: given
Matrix: (-0.978913479386, -0.147734662348, 0.14107752981), (-0.142616603126, 0.988718657719, 0.0457812231264), (-0.146249459449, 0.0246958583422, -0.98893943707)
Vector: 96.4604952541, 6.70661344139, -42.2983157043)

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 54702.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tacheng Tick Virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C0C9F4
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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Lithium sulfate monohydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 20% w/v Polyethylene glycol 1,000

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. obs: 35656 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.993 / Net I/σ(I): 12.4
Reflection shellResolution: 2.52→2.67 Å / Num. unique obs: 35627 / CC1/2: 0.873

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→50 Å / SU ML: 0.4451 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.7893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2725 1740 4.88 %
Rwork0.2233 33896 -
obs0.2256 35627 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.82 Å2
Refinement stepCycle: LAST / Resolution: 2.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7351 0 0 0 7351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01027527
X-RAY DIFFRACTIONf_angle_d1.151310188
X-RAY DIFFRACTIONf_chiral_restr0.05841111
X-RAY DIFFRACTIONf_plane_restr0.00911288
X-RAY DIFFRACTIONf_dihedral_angle_d5.9127992
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.51469815966 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.590.37971310.32882812X-RAY DIFFRACTION98.3
2.59-2.680.36411400.32682773X-RAY DIFFRACTION98.25
2.68-2.770.35991520.32032778X-RAY DIFFRACTION98.12
2.77-2.880.41871650.33222826X-RAY DIFFRACTION99.53
2.88-3.020.39761560.2972821X-RAY DIFFRACTION99.9
3.02-3.170.33891320.28172846X-RAY DIFFRACTION99.83
3.17-3.370.31261420.28762852X-RAY DIFFRACTION99.73
3.37-3.630.28291530.23072792X-RAY DIFFRACTION98.36
3.63-40.25421280.20132794X-RAY DIFFRACTION97.56
4-4.580.2351510.1752843X-RAY DIFFRACTION99.01
4.58-5.760.19071420.16852889X-RAY DIFFRACTION99.87
5.76-44.220.2271480.17742870X-RAY DIFFRACTION97.92
Refinement TLS params.Method: refined / Origin x: 45.5603927466 Å / Origin y: -0.573760758915 Å / Origin z: -23.7672226058 Å
111213212223313233
T0.49541709922 Å2-0.00596358458189 Å20.0502616313837 Å2-0.409959609437 Å20.0620812131911 Å2--0.466139192105 Å2
L0.633259390727 °2-0.0115267971433 °20.710878968709 °2--0.00289864207631 °20.144758962309 °2--0.252316541103 °2
S0.0732892775271 Å °0.0399149904193 Å °-0.0759307183398 Å °-0.0460032969288 Å °-0.0192097251323 Å °0.0394713061606 Å °0.100325699137 Å °0.0728545632506 Å °-0.0507156409087 Å °
Refinement TLS groupSelection details: all

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