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- PDB-8fuq: Crystal structure of rabies virus (strain CVS-11) P3 dimerization... -

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Basic information

Entry
Database: PDB / ID: 8fuq
TitleCrystal structure of rabies virus (strain CVS-11) P3 dimerization domain
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / rabies / phosphoprotein / lyssavirus / chaperone
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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / host cell / 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 ...: / microtubule-dependent intracellular transport of viral material towards nucleus / 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 / host cell / 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 / RNA-directed RNA polymerase activity / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Phosphoprotein / Phosphoprotein, C-terminal / : / Phosphoprotein
Similarity search - Domain/homology
Biological speciesLyssavirus rabies
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDonnelly, C.M. / Cross, E.M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of rabies virus (strain CVS-11) P3 dimerization domain
Authors: Donnelly, C.M. / Cross, E.M. / Forwood, J.K.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
F: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)82,4236
Polymers82,4236
Non-polymers00
Water3,045169
1
A: Phosphoprotein
B: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)27,4742
Polymers27,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-23 kcal/mol
Surface area6240 Å2
MethodPISA
2
C: Phosphoprotein
D: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)27,4742
Polymers27,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-20 kcal/mol
Surface area6110 Å2
MethodPISA
3
E: Phosphoprotein
F: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)27,4742
Polymers27,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-23 kcal/mol
Surface area5790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.050, 44.097, 111.787
Angle α, β, γ (deg.)90.000, 100.440, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-226-

HOH

21C-230-

HOH

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Components

#1: Protein
Phosphoprotein / Protein P / Protein M1


Mass: 13737.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus rabies / Strain: CVS-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15198
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 0.99 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium nitrate, 0.1 M Bis-Tris propane, 20 % w/v PEG 3350

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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 EIGER2 S 16M / Detector: PIXEL / Date: Sep 15, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→52.53 Å / Num. obs: 30167 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.21 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.156 / Net I/σ(I): 2.9
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.521 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1797 / CC1/2: 0.248 / Rpim(I) all: 2.753

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Processing

Software
NameVersionClassification
PHASER1.20.1_4487phasing
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→52.51 Å / SU ML: 0.2774 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.5342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2372 1499 4.97 %
Rwork0.2076 28666 -
obs0.2091 30165 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→52.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 0 169 2575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01532489
X-RAY DIFFRACTIONf_angle_d1.5593394
X-RAY DIFFRACTIONf_chiral_restr0.09384
X-RAY DIFFRACTIONf_plane_restr0.0301439
X-RAY DIFFRACTIONf_dihedral_angle_d19.3941921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.37761310.34442529X-RAY DIFFRACTION97.9
1.85-1.920.38591410.32312585X-RAY DIFFRACTION99.63
1.92-20.31821370.29792612X-RAY DIFFRACTION100
2-2.090.30251260.25772584X-RAY DIFFRACTION100
2.09-2.20.30061470.23052583X-RAY DIFFRACTION99.96
2.2-2.340.22511370.20532601X-RAY DIFFRACTION99.93
2.34-2.520.22711420.19712596X-RAY DIFFRACTION99.96
2.52-2.770.24121340.1942629X-RAY DIFFRACTION100
2.77-3.170.22561280.18972616X-RAY DIFFRACTION99.71
3.17-3.990.20611380.17232633X-RAY DIFFRACTION99.89
4-52.510.19081380.18962698X-RAY DIFFRACTION99.79

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