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- PDB-7pno: C terminal domain of Nipah Virus Phosphoprotein fused to the Ntai... -

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Basic information

Entry
Database: PDB / ID: 7pno
TitleC terminal domain of Nipah Virus Phosphoprotein fused to the Ntail alpha more of the Nucleoprotein.
Components
  • Phosphoprotein
  • alpha MoRE of Nipah virus Nucleoprotein tail
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 / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 ...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 / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesNipah virus
Nipah henipavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.79 Å
AuthorsBourhis, J.M. / Yabukaski, F. / Tarbouriech, N. / Jamin, 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 7, 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

Downloads & links

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Assembly

Deposited unit
A: Phosphoprotein
B: alpha MoRE of Nipah virus Nucleoprotein tail
C: Phosphoprotein
D: alpha MoRE of Nipah virus Nucleoprotein tail
E: Phosphoprotein
F: alpha MoRE of Nipah virus Nucleoprotein tail
G: Phosphoprotein
H: alpha MoRE of Nipah virus Nucleoprotein tail
I: Phosphoprotein
J: alpha MoRE of Nipah virus Nucleoprotein tail
K: Phosphoprotein
L: alpha MoRE of Nipah virus Nucleoprotein tail
M: Phosphoprotein
N: alpha MoRE of Nipah virus Nucleoprotein tail


Theoretical massNumber of molelcules
Total (without water)71,49214
Polymers71,49214
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15380 Å2
ΔGint-34 kcal/mol
Surface area24360 Å2
Unit cell
Length a, b, c (Å)60.460, 131.970, 156.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Phosphoprotein / Protein P


Mass: 6306.980 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah virus / Gene: P/V/C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9IK91
#2: Protein/peptide
alpha MoRE of Nipah virus Nucleoprotein tail


Mass: 3906.196 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nipah henipavirus / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 20% PEG 550, Sodium acetate 100 mM pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9394 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 2.8→78.45 Å / Num. obs: 16111 / % possible obs: 99.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.1
Reflection shellResolution: 2.8→2.98 Å / Rmerge(I) obs: 0.349 / Num. unique obs: 2844

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
AMPLEphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.79→23.94 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 24.726 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 5.123 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25743 808 5 %RANDOM
Rwork0.2029 ---
obs0.20548 15240 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.275 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2--0.08 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.79→23.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 0 14 3798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193784
X-RAY DIFFRACTIONr_bond_other_d0.0010.023840
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9795066
X-RAY DIFFRACTIONr_angle_other_deg0.80538799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0995472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97424.759187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57815766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3141542
X-RAY DIFFRACTIONr_chiral_restr0.0790.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
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_it2.3223.7191930
X-RAY DIFFRACTIONr_mcbond_other2.323.7181929
X-RAY DIFFRACTIONr_mcangle_it3.7485.5482388
X-RAY DIFFRACTIONr_mcangle_other3.7485.5492389
X-RAY DIFFRACTIONr_scbond_it3.2364.0411853
X-RAY DIFFRACTIONr_scbond_other3.2374.0391851
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2715.8862678
X-RAY DIFFRACTIONr_long_range_B_refined6.8128.124405
X-RAY DIFFRACTIONr_long_range_B_other6.80928.1274406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.79→2.856 Å
RfactorNum. reflection% reflection
Rfree0.295 42 -
Rwork0.306 1099 -
obs--98.96 %
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)
14.69640.54041.58265.0810.20573.03090.08360.22150.0886-0.3335-0.10090.394-0.0392-0.25730.01730.1903-0.09440.01910.15290.01650.2343-46.035-20.22910.936
26.33762.90455.22374.1588-0.85818.6902-0.66020.12250.8031-0.5602-0.16740.4388-0.3508-0.13090.82760.30960.0685-0.0770.4853-0.00710.5251-52.621-10.5965.537
34.9688-0.4638-0.622.90220.29544.9033-0.0426-0.063-0.11980.0039-0.15760.02510.0067-0.20320.20020.1713-0.06840.02260.046-0.01760.0566-27.12516.94623.612
413.0626-3.0164-7.93954.56170.52585.50320.39560.2452-0.0799-0.1549-0.270.1304-0.5164-0.1004-0.12550.39470.00230.04410.2826-0.04550.1154-28.32524.51134.149
54.88390.0671-0.80814.8931.32893.42280.01040.3751-0.1567-0.3886-0.0739-0.20440.04460.17140.06350.1962-0.1006-0.00270.1509-0.00610.1211-17.9623.9638.222
66.9549-0.3414-6.50962.0593.531312.0468-0.18020.2391-0.2236-0.46090.02840.0728-0.47170.44740.15190.4853-0.0024-0.03980.47310.06910.3039-15.95529.481-3.862
75.3979-0.0116-0.52214.1697-0.74344.34940.0973-0.4981-0.21690.2265-0.1831-0.10590.02130.02450.08580.1552-0.1095-0.01540.1209-0.00850.1675-11.90132.58124.417
82.72840.9728-1.34553.4787-0.888413.544-0.0313-0.2491-0.24430.3543-0.3137-0.1333-0.4776-0.23280.34510.3562-0.0044-0.06890.60050.02190.3562-3.47935.42233.826
95.0457-1.36811.11285.7387-0.70933.33070.0139-0.3014-0.38260.0724-0.1524-0.29280.160.31190.13850.1775-0.11130.03350.16650.03050.2271-29.048-16.57619.241
1017.4667-1.46944.2391.07081.23954.14240.0595-0.04960.57930.219-0.0424-0.51080.3214-0.2528-0.01710.4138-0.1939-0.06850.61290.16420.845-16.695-15.2118.621
115.22081.06870.6024.97190.4793.73020.0688-0.19870.16820.1062-0.28390.41840.1037-0.34980.2150.1501-0.07170.06430.1029-0.04380.2639-39.41-0.40917.965
1215.5288-6.0612-0.67044.5242-1.0890.88130.35460.25190.5627-0.1482-0.10150.28160.0292-0.0294-0.25310.5540.0096-0.0010.6999-0.1090.6169-45.3769.10423.473
134.8524-0.6048-0.68973.93951.79894.09770.0872-0.1522-0.07960.1354-0.206-0.04350.21330.11610.11880.1253-0.07670.00990.08140.00030.103-21.1712.51912.188
149.1972-4.8286-1.316211.56473.64351.35040.1323-0.4850.5994-0.29680.1563-0.88480.07150.33-0.28860.33410.11440.07990.56650.02820.3407-11.3553.894.016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A659 - 707
2X-RAY DIFFRACTION2B469 - 491
3X-RAY DIFFRACTION3C659 - 707
4X-RAY DIFFRACTION4D469 - 492
5X-RAY DIFFRACTION5E659 - 707
6X-RAY DIFFRACTION6F470 - 492
7X-RAY DIFFRACTION7G659 - 707
8X-RAY DIFFRACTION8H470 - 490
9X-RAY DIFFRACTION9I659 - 707
10X-RAY DIFFRACTION10J473 - 486
11X-RAY DIFFRACTION11K659 - 707
12X-RAY DIFFRACTION12L471 - 488
13X-RAY DIFFRACTION13M659 - 707
14X-RAY DIFFRACTION14N471 - 490

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