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- PDB-9up1: Tacheng tick virus 1 nucleoprotein-Nucle acid complex -

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Basic information

Entry
Database: PDB / ID: 9up1
TitleTacheng tick virus 1 nucleoprotein-Nucle acid complex
Components
  • DNA (5'-D(P*CP*CP*TP*CP*CP*CP*GP*CP*AP*CP*TP*TP*C)-3')
  • DNA (5'-D(P*CP*GP*TP*AP*AP*TP*CP*C)-3')
  • Nucleoprotein
KeywordsVIRAL PROTEIN/DNA / Nairovirus / Nucleprotein / Complex / VIRAL PROTEIN-DNA complex
Function / homologyNucleocapsid N protein / Nucleocapsid N protein / helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / RNA binding / DNA / DNA (> 10) / Nucleoprotein
Function and homology information
Biological speciesTacheng Tick Virus 1
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, Z. / Sun, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Tacheng tick virus 1 nucleoprotein-Nucle acid complex
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
C: DNA (5'-D(P*CP*CP*TP*CP*CP*CP*GP*CP*AP*CP*TP*TP*C)-3')
D: DNA (5'-D(P*CP*GP*TP*AP*AP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)115,6144
Polymers115,6144
Non-polymers00
Water1,982110
1
A: Nucleoprotein
C: DNA (5'-D(P*CP*CP*TP*CP*CP*CP*GP*CP*AP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)58,5262
Polymers58,5262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-23 kcal/mol
Surface area21940 Å2
MethodPISA
2
B: Nucleoprotein
D: DNA (5'-D(P*CP*GP*TP*AP*AP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)57,0892
Polymers57,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-11 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.769, 60.242, 96.018
Angle α, β, γ (deg.)90.000, 93.008, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 2 through 181 or resid 195 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_11ALAALAALAALAAA2 - 1812 - 181
d_12HISHISGLYGLYAA195 - 299195 - 299
d_13PHEPHETYRTYRAA301 - 486301 - 486
d_21ALAALAALAALABB2 - 1812 - 181
d_22HISHISTYRTYRBB195 - 486195 - 486

NCS oper: (Code: givenMatrix: (-0.0261653349907, -0.0158181966691, 0.999532470658), (-0.0773631838644, 0.99690813742, 0.0137514845795), (-0.996659577302, -0.0769672021052, -0.0273081814279)Vector: -1. ...NCS oper: (Code: given
Matrix: (-0.0261653349907, -0.0158181966691, 0.999532470658), (-0.0773631838644, 0.99690813742, 0.0137514845795), (-0.996659577302, -0.0769672021052, -0.0273081814279)
Vector: -1.82078906061, -13.4670615795, 91.1919738374)

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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
#2: DNA chain DNA (5'-D(P*CP*CP*TP*CP*CP*CP*GP*CP*AP*CP*TP*TP*C)-3')


Mass: 3823.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: DNA chain DNA (5'-D(P*CP*GP*TP*AP*AP*TP*CP*C)-3')


Mass: 2386.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium formate, 0.1 M BICINE pH 8.5, 20% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 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: 2.5→50 Å / Num. obs: 35981 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.968 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 35981 / CC1/2: 0.968

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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: 2.5→33.42 Å / SU ML: 0.3817 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.1019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2669 1715 4.77 %
Rwork0.199 34226 -
obs0.2025 35941 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7377 416 0 110 7903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00968014
X-RAY DIFFRACTIONf_angle_d1.179310925
X-RAY DIFFRACTIONf_chiral_restr0.05621199
X-RAY DIFFRACTIONf_plane_restr0.00941313
X-RAY DIFFRACTIONf_dihedral_angle_d14.24661199
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.87691646649 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.3511360.27692766X-RAY DIFFRACTION97.25
2.58-2.660.33921200.27742871X-RAY DIFFRACTION99.77
2.66-2.760.3911220.26492855X-RAY DIFFRACTION99.93
2.76-2.870.34031370.24142830X-RAY DIFFRACTION99.93
2.87-30.29451270.23452864X-RAY DIFFRACTION99.93
3-3.150.30451220.2372847X-RAY DIFFRACTION99.97
3.15-3.350.32551560.23752852X-RAY DIFFRACTION100
3.35-3.610.27371410.2052837X-RAY DIFFRACTION100
3.61-3.970.29311480.17812856X-RAY DIFFRACTION100
3.97-4.550.21561600.15682875X-RAY DIFFRACTION100
4.55-5.720.20681540.17312867X-RAY DIFFRACTION99.97
5.73-33.420.23891920.17212906X-RAY DIFFRACTION99.52
Refinement TLS params.Method: refined / Origin x: 34.9264578428 Å / Origin y: 10.346210673 Å / Origin z: 27.8228371262 Å
111213212223313233
T0.390858080447 Å20.0472943684373 Å2-0.00526863863698 Å2-0.354929719136 Å2-0.0144523731715 Å2--0.368922013057 Å2
L0.928308178811 °20.404683291453 °2-0.0622134344414 °2-0.274786958889 °2-0.0203525823947 °2--0.329384288551 °2
S-0.0294558880782 Å °0.320252057381 Å °0.0118042914271 Å °-0.020233397125 Å °0.0813500306456 Å °-0.011768550725 Å °-0.0454806193211 Å °-0.0220260361033 Å °-0.0457340047635 Å °
Refinement TLS groupSelection details: all

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