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- PDB-8rcq: Structural flexibility of Nucleoprotein of the Toscana virus in t... -

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Basic information

Entry
Database: PDB / ID: 8rcq
TitleStructural flexibility of Nucleoprotein of the Toscana virus in the presence of a nanobody.
Components
  • Nucleoprotein
  • VHH
KeywordsVIRAL PROTEIN / Toscana virus / Nucleoprotein / SAXS / VHH / nanobody / drugs
Function / homology
Function and homology information


helical viral capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesToscana virus
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsPapageorgiou, N. / Ferron, F. / Coutard, B. / Lichiere, J. / Baklouti, A.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-BSV8-0019 France
Agence Nationale de la Recherche (ANR)ANR-10-INSB-05-01 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Structural flexibility of Toscana virus nucleoprotein in the presence of a single-chain camelid antibody.
Authors: Papageorgiou, N. / Baklouti, A. / Lichiere, J. / Desmyter, A. / Canard, B. / Coutard, B. / Ferron, F.
History
DepositionDec 6, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionJan 31, 2024ID: 8BPK
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: VHH


Theoretical massNumber of molelcules
Total (without water)42,6152
Polymers42,6152
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.755, 54.755, 380.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 27665.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toscana virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21701
#2: Antibody VHH


Mass: 14948.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5M MES, pH 6.5, 25% w/v PEG 2000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.8→47.46 Å / Num. obs: 6413 / % possible obs: 99.47 % / Redundancy: 10.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.06 / Rrim(I) all: 0.21 / Net I/av σ(I): 12 / Net I/σ(I): 12
Reflection shellResolution: 3.8→3.97 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 6413 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→47.46 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.35 1071 9.87 %Random
Rwork0.3 ---
obs-6413 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 0 0 2763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032805
X-RAY DIFFRACTIONf_angle_d0.5973781
X-RAY DIFFRACTIONf_dihedral_angle_d4.022392
X-RAY DIFFRACTIONf_chiral_restr0.039427
X-RAY DIFFRACTIONf_plane_restr0.004486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.970.46651350.45441215X-RAY DIFFRACTION98
3.97-4.180.48491330.40761236X-RAY DIFFRACTION100
4.18-4.440.47181370.37281187X-RAY DIFFRACTION99
4.44-4.790.3551321224X-RAY DIFFRACTION99
4.79-5.270.48591290.39491242X-RAY DIFFRACTION100
5.27-6.030.35661430.35581231X-RAY DIFFRACTION100
6.03-7.590.3251360.30891218X-RAY DIFFRACTION100
7.59-100.27331260.21851227X-RAY DIFFRACTION99

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