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- PDB-7t5h: Structure of rabies virus phosphoprotein C-terminal domain, wild type -

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Basic information

Entry
Database: PDB / ID: 7t5h
TitleStructure of rabies virus phosphoprotein C-terminal domain, wild type
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / rabies / phosphoprotein / virus / lyssavirus
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / host cell / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...microtubule-dependent intracellular transport of viral material towards nucleus / viral transcription / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / host cell / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / host cell nucleus
Similarity search - Function
: / Phosphoprotein / Phosphoprotein, C-terminal / Phosphoprotein
Similarity search - Domain/homology
PHOSPHATE ION / Phosphoprotein
Similarity search - Component
Biological speciesRabies virus Nishigahara RCEH
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhan, J. / Metcalfe, R.D. / Gooley, P.R. / Griffin, M.D.W.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1125704 Australia
Australian Research Council (ARC)DP210100998 Australia
CitationJournal: J.Virol. / Year: 2022
Title: Molecular Basis of Functional Effects of Phosphorylation of the C-Terminal Domain of the Rabies Virus P Protein.
Authors: Zhan, J. / Watts, E. / Brice, A.M. / Metcalfe, R.D. / Rozario, A.M. / Sethi, A. / Yan, F. / Bell, T.D.M. / Griffin, M.D.W. / Moseley, G.W. / Gooley, P.R.
History
DepositionDec 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3685
Polymers13,0191
Non-polymers3494
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.312, 43.987, 61.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Phosphoprotein / / Protein P / Protein M1


Mass: 13018.811 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: C297S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies virus Nishigahara RCEH / Strain: Nishigahara RCEH / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9IPJ8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 4.75
Details: 1.9 M ammonium sulfate, 0.2 M potassium sodium tartrate and 0.1 M sodium citrate (pH 4.75)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→43.99 Å / Num. obs: 18982 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 14.9
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 1.463 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 928 / CC1/2: 0.816 / Rpim(I) all: 0.411 / Rrim(I) all: 1.544

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vyi

1vyi


Resolution: 1.5→34.83 Å / SU ML: 0.1384 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 22.9442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2114 949 5.02 %
Rwork0.1853 17963 -
obs0.1866 18912 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 19 103 983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068902
X-RAY DIFFRACTIONf_angle_d0.87251214
X-RAY DIFFRACTIONf_chiral_restr0.0403131
X-RAY DIFFRACTIONf_plane_restr0.0105156
X-RAY DIFFRACTIONf_dihedral_angle_d12.1985341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.28531440.25182510X-RAY DIFFRACTION99.85
1.58-1.680.26781190.27432525X-RAY DIFFRACTION99.89
1.68-1.810.25941400.21462530X-RAY DIFFRACTION99.74
1.81-1.990.25311430.21342533X-RAY DIFFRACTION99.96
1.99-2.280.21861460.18332555X-RAY DIFFRACTION99.82
2.28-2.870.1581020.18182609X-RAY DIFFRACTION99.96
2.87-34.830.20721550.16852701X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 0.205659003875 Å / Origin y: -9.76543998279 Å / Origin z: 11.4348981287 Å
111213212223313233
T0.157477616968 Å20.022016912167 Å2-0.00275567713029 Å2-0.12219138266 Å2-0.00722882842289 Å2--0.10190257267 Å2
L4.0140918379 °21.70154180164 °2-0.269496559525 °2-3.43214964851 °2-0.680794675932 °2--2.03711488051 °2
S-0.119464040058 Å °0.00363896151351 Å °0.00259540559049 Å °-0.0250994529141 Å °0.0875489397664 Å °0.0637799281462 Å °-0.129451036289 Å °-0.0859297317971 Å °0.0332735120013 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 190 through 297)

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