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- PDB-8b8v: Crystal structure of the Rabies virus RNA free nucleoprotein- pho... -

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Basic information

Entry
Database: PDB / ID: 8b8v
TitleCrystal structure of the Rabies virus RNA free nucleoprotein- phosphoprotein complex
Components
  • Nucleoprotein
  • Phosphoprotein
KeywordsVIRAL PROTEIN / CHAPERONE / Complex / Replication machinery / virus
Function / homology
Function and homology information


helical viral capsid / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / RNA-dependent RNA polymerase activity ...helical viral capsid / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / RNA-dependent RNA polymerase activity / RNA binding / cytoplasm
Similarity search - Function
Phosphoprotein / Phosphoprotein, C-terminal / Phosphoprotein / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phosphoprotein / Nucleoprotein
Similarity search - Component
Biological speciesLyssavirus rabies
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsGerard, F.C.A. / Jamin, M. / Bourhis, J.M.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-BSV8-2012-NNViPol France
Foundation for Medical Research (France)Equipe 2017 DEQ20170336754 France
CitationJournal: Viruses / Year: 2022
Title: Structure and Dynamics of the Unassembled Nucleoprotein of Rabies Virus in Complex with Its Phosphoprotein Chaperone Module.
Authors: Gerard, F.C.A. / Bourhis, J.M. / Mas, C. / Branchard, A. / Vu, D.D. / Varhoshkova, S. / Leyrat, C. / Jamin, M.
History
DepositionOct 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_src_gen / pdbx_initial_refinement_model
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8183
Polymers56,7122
Non-polymers1061
Water84747
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-13 kcal/mol
Surface area18050 Å2
Unit cell
Length a, b, c (Å)39.571, 73.617, 154.361
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 48210.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus rabies / Strain: CVS-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: D6Q0Q6
#2: Protein Phosphoprotein / Protein P / Protein M1


Mass: 8501.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus rabies / Strain: CVS-11 / Gene: NS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: A8VR26
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.02M sodium/potassium phosphate, 0.1M Bis Tris propane pH 6.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19735 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.31
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.76 / Num. unique obs: 1397

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gtt

2gtt


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.694 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1050 5.1 %RANDOM
Rwork0.1782 ---
obs0.1807 19735 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.68 Å2 / Biso mean: 33.577 Å2 / Biso min: 14.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 7 47 3196
Biso mean--42.83 28.8 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193219
X-RAY DIFFRACTIONr_bond_other_d0.0060.023051
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9474347
X-RAY DIFFRACTIONr_angle_other_deg1.0637005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17223.129147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31515542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8671522
X-RAY DIFFRACTIONr_chiral_restr0.1070.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023606
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02776
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 68 -
Rwork0.209 1397 -
all-1465 -
obs--98.85 %

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