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- PDB-8b8a: Multimerization domain of borna disease virus 1 phosphoprotein -

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Basic information

Entry
Database: PDB / ID: 8b8a
TitleMultimerization domain of borna disease virus 1 phosphoprotein
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / phosphoprotein / RNA polymerase cofactor
Function / homologyBorna disease virus P24 / Borna disease virus P24 protein / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / Phosphoprotein
Function and homology information
Biological speciesBorna disease virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsTarbouriech, N. / Legrand, P. / Bourhis, J.M. / Chenavier, F. / Freslon, L. / Kawasaki, J. / Horie, M. / Tomonaga, K. / Bachiri, K. / Coyaud, E. ...Tarbouriech, N. / Legrand, P. / Bourhis, J.M. / Chenavier, F. / Freslon, L. / Kawasaki, J. / Horie, M. / Tomonaga, K. / Bachiri, K. / Coyaud, E. / Gonzalez-Dunia, D. / Ruigrok, R.W.H. / 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 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)12,2231
Polymers12,2231
Non-polymers00
Water32418
1
A: Phosphoprotein

A: Phosphoprotein

A: Phosphoprotein

A: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)48,8924
Polymers48,8924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area16250 Å2
ΔGint-201 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.271, 35.271, 166.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

21A-212-

HOH

31A-216-

HOH

41A-217-

HOH

51A-218-

HOH

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Components

#1: Protein Phosphoprotein / P protein / p23 / p24


Mass: 12223.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus 1 / Gene: P/X / Plasmid: pETM11 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): RIL / References: UniProt: P0C798
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: fine plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM HEPES pH 7.5, 14-18 % polyethylene glycol 8K, 200 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97717 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97717 Å / Relative weight: 1
ReflectionResolution: 2.75→55 Å / Num. obs: 3173 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 80.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.258 / Rpim(I) all: 0.108 / Net I/σ(I): 5
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 11.8 % / Rmerge(I) obs: 3.26 / Num. unique obs: 214 / CC1/2: 0.601 / Rpim(I) all: 1.357 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.10.3 (3-OCT-2019)refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bhv

4bhv


Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.855 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.507
RfactorNum. reflection% reflectionSelection details
Rfree0.307 140 5.3 %RANDOM
Rwork0.2552 ---
obs0.2578 2642 83.6 %-
Displacement parametersBiso max: 145.5 Å2 / Biso mean: 80.02 Å2 / Biso min: 28.55 Å2
Baniso -1Baniso -2Baniso -3
1--7.6732 Å20 Å20 Å2
2---7.6732 Å20 Å2
3---15.3465 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: final / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms739 0 0 9 748
Biso mean---44.75 -
Num. residues----95
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d291SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes125HARMONIC5
X-RAY DIFFRACTIONt_it741HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion107SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact627SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d741HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg991HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion20.59
LS refinement shellResolution: 2.75→3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3463 24 6.35 %
Rwork0.242 354 -
all0.2484 378 -
obs--49.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.96830.2551.21941.62871.21887.2055-0.04640.43530.1835-0.5395-0.04760.17420.0093-0.10960.0941-0.08990.0894-0.0178-0.21140.06680.30411.80774.5676-32.7246
23.63110.01421.60791.66951.67627.891-0.0389-0.54420.21690.21940.0883-0.27020.12850.2496-0.0495-0.0751-0.06410.0398-0.1534-0.12660.199122.60724.391840.9538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|53 }A1 - 53
2X-RAY DIFFRACTION2{ A|54 - A|95 }A54 - 95

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