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- PDB-8b8d: multimerization domain of Gaboon Viper Virus 1 -

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Basic information

Entry
Database: PDB / ID: 8b8d
Titlemultimerization domain of Gaboon Viper Virus 1
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / phosphoprotein / RNA polymerase cofactor
Function / homologyBorna disease virus P24 / Borna disease virus P24 protein / Phosphoprotein
Function and homology information
Biological speciesGaboon viper virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsTarbouriech, N. / Legrand, P. / Bouhris, J.M. / Horie, M. / Tomonaga, K. / Crepin, T.
Funding support France, Japan, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE15-0026 France
Japan Society for the Promotion of Science (JSPS)JP21H01199 Japan
CitationJournal: Viruses / Year: 2022
Title: Borna Disease Virus 1 Phosphoprotein Forms a Tetramer and Interacts with Host Factors Involved in DNA Double-Strand Break Repair and mRNA Processing.
Authors: Tarbouriech, N. / Chenavier, F. / Kawasaki, J. / Bachiri, K. / Bourhis, J.M. / Legrand, P. / Freslon, L.L. / Laurent, E.M.N. / Suberbielle, E. / Ruigrok, R.W.H. / Tomonaga, K. / Gonzalez- ...Authors: Tarbouriech, N. / Chenavier, F. / Kawasaki, J. / Bachiri, K. / Bourhis, J.M. / Legrand, P. / Freslon, L.L. / Laurent, E.M.N. / Suberbielle, E. / Ruigrok, R.W.H. / Tomonaga, K. / Gonzalez-Dunia, D. / Horie, M. / Coyaud, E. / Crepin, T.
History
DepositionOct 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)51,6834
Polymers51,6834
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, assayed by SEC-SAXS, MALLS and gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18350 Å2
ΔGint-186 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.824, 82.499, 89.057
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Phosphoprotein


Mass: 12920.860 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gaboon viper virus 1 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL / References: UniProt: L0N429
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 18-22 % PEG 3350, 200 mM NaSCN

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.978565
SYNCHROTRONSOLEIL PROXIMA 220.98919
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELOct 9, 2021
DECTRIS EIGER X 9M2PIXELDec 10, 2021
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9785651
20.989191
Reflection

Entry-ID: 8B8D / CC1/2: 0.999

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.4-492410899.613.50.1140.046111.4
2.79-481517099.210.2210.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
2.4-2.4613.917420.62199.4
2.79-2.87109880.657289.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.71 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.234 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.505 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3106 1020 5.3 %RANDOM
Rwork0.2283 ---
obs0.2329 18296 79.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.63 Å2 / Biso mean: 52.184 Å2 / Biso min: 10.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.41 Å2-0 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 2.4→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 0 151 3375
Biso mean---47.38 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173262
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.6324341
X-RAY DIFFRACTIONr_angle_other_deg1.2381.5797621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1665399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72725152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.75115730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8141516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02515
LS refinement shellResolution: 2.4→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.513 15 -
Rwork0.286 449 -
all-464 -
obs--26.44 %

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