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- PDB-7pon: C TERMINAL DOMAIN OF NIPAH VIRUS PHOSPHOPROTEIN -

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Basic information

Entry
Database: PDB / ID: 7pon
TitleC TERMINAL DOMAIN OF NIPAH VIRUS PHOSPHOPROTEIN
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / NIPAH VIRUS / PHOSPHOPROTEIN / polymerase cofactor
Function / homology
Function and homology information


negative stranded viral RNA transcription / negative stranded viral RNA replication / virion component / molecular adaptor activity / host cell cytoplasm / symbiont-mediated suppression of host innate immune response
Similarity search - Function
Phosphoprotein P region PNT disordered / Phosphoprotein P region PNT disordered / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / Phosphoprotein P soyouz module / N-terminal region of Paramyxovirinae phosphoprotein (P) / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal
Similarity search - Domain/homology
Biological speciesNipah virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsYabukarski, F. / Tarbouriech, N. / Jamin, M. / Bourhis, J.M.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-BSV8-2012-NNViPol France
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0014-02 France
Foundation for Medical Research (France)DEQ20170336754 France
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Dynamics of the C-terminal X Domain of Nipah and Hendra Viruses Controls the Attachment to the C-terminal Tail of the Nucleocapsid Protein.
Authors: Bourhis, J.M. / Yabukarski, F. / Communie, G. / Schneider, R. / Volchkova, V.A. / Freneat, M. / Gerard, F.C. / Ducournau, C. / Mas, C. / Tarbouriech, N. / Ringkjobing Jensen, M. / Volchkov, ...Authors: Bourhis, J.M. / Yabukarski, F. / Communie, G. / Schneider, R. / Volchkova, V.A. / Freneat, M. / Gerard, F.C. / Ducournau, C. / Mas, C. / Tarbouriech, N. / Ringkjobing Jensen, M. / Volchkov, V.E. / Blackledge, M. / Jamin, M.
History
DepositionSep 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 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


Theoretical massNumber of molelcules
Total (without water)7,3781
Polymers7,3781
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.319, 35.319, 112.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phosphoprotein / Protein P


Mass: 7378.133 Da / Num. of mol.: 1 / Fragment: C TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Gene: P/V/C / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 ROSETTA / References: UniProt: Q9IK91
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M BIS-TRIS, 25% PEG 3350, 0.2M MAGNESIUM CHLORIDE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07189 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2011 / Details: MIRROR
RadiationMonochromator: SILICON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07189 Å / Relative weight: 1
ReflectionResolution: 2.1→37.63 Å / Num. obs: 4643 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.019 / Net I/σ(I): 23.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2364 / Rpim(I) all: 0.234 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→33.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 14.201 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27314 459 10 %RANDOM
Rwork0.22509 ---
obs0.22987 4139 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.129 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å2-0 Å2-0 Å2
2--2.27 Å2-0 Å2
3----4.54 Å2
Refinement stepCycle: 1 / Resolution: 2.1→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 0 12 452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.013476
X-RAY DIFFRACTIONr_bond_other_d0.0010.017454
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.642646
X-RAY DIFFRACTIONr_angle_other_deg1.4621.6041059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.777562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.4823.33333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.371598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.167155
X-RAY DIFFRACTIONr_chiral_restr0.1040.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02548
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0291
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4364.521233
X-RAY DIFFRACTIONr_mcbond_other3.3584.513232
X-RAY DIFFRACTIONr_mcangle_it4.8276.712294
X-RAY DIFFRACTIONr_mcangle_other4.8266.727295
X-RAY DIFFRACTIONr_scbond_it4.6364.997243
X-RAY DIFFRACTIONr_scbond_other4.6265.009244
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8257.347351
X-RAY DIFFRACTIONr_long_range_B_refined8.50252.123517
X-RAY DIFFRACTIONr_long_range_B_other8.49652.142517
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 25 -
Rwork0.287 304 -
obs--98.21 %
Refinement TLS params.Method: refined / Origin x: 9.509 Å / Origin y: 13.106 Å / Origin z: 44.69 Å
111213212223313233
T0.2041 Å20.0334 Å2-0.0348 Å2-0.1506 Å20.036 Å2--0.0542 Å2
L0.1214 °20.4149 °2-0.8135 °2-1.7879 °2-2.5525 °2--5.8869 °2
S-0.0235 Å °0.0059 Å °-0.0188 Å °-0.1394 Å °-0.1581 Å °-0.0286 Å °-0.1452 Å °-0.15 Å °0.1816 Å °

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