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- PDB-7t5g: Structure of rabies virus phosphoprotein C-terminal domain, S210E... -

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Basic information

Entry
Database: PDB / ID: 7t5g
TitleStructure of rabies virus phosphoprotein C-terminal domain, S210E mutant
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 / 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 ...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 / symbiont entry into host cell / RNA-directed RNA polymerase activity / host cell nucleus
Similarity search - Function
Phosphoprotein / Phosphoprotein, C-terminal / : / Phosphoprotein
Similarity search - Domain/homology
Biological speciesRabies virus Nishigahara RCEH
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: Phosphoprotein
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6027
Polymers26,1222
Non-polymers4805
Water1,26170
1
A: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3494
Polymers13,0611
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2533
Polymers13,0611
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.704, 69.089, 75.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Phosphoprotein / Protein P / Protein M1


Mass: 13060.847 Da / Num. of mol.: 2 / Fragment: C-terminal domain / Mutation: S210E, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
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

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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 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: 1.696→38.49 Å / Num. obs: 14479 / % possible obs: 54.24 % / Redundancy: 12.91 % / Biso Wilson estimate: 26.26 Å2 / CC1/2: 0.9976 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.032 / Rrim(I) all: 0.116 / Net I/σ(I): 13.086
Reflection shellResolution: 1.696→1.868 Å / Redundancy: 11.35 % / Rmerge(I) obs: 1.68 / Mean I/σ(I) obs: 1.862 / Num. unique obs: 724 / CC1/2: 0.6152 / Rpim(I) all: 0.505 / Rrim(I) all: 1.757 / % possible all: 10.94

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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: 1.7→38.49 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.6994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2443 688 4.83 %
Rwork0.2045 13551 -
obs0.2065 14239 53.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 25 70 1816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211773
X-RAY DIFFRACTIONf_angle_d0.44132390
X-RAY DIFFRACTIONf_chiral_restr0.0317262
X-RAY DIFFRACTIONf_plane_restr0.0023306
X-RAY DIFFRACTIONf_dihedral_angle_d12.6881668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.3553200.3364442X-RAY DIFFRACTION8.82
1.83-2.010.3489600.2861173X-RAY DIFFRACTION23.45
2.01-2.30.2961330.28092524X-RAY DIFFRACTION50.23
2.3-2.90.2891920.23964146X-RAY DIFFRACTION81.37
2.9-38.490.21982830.17615266X-RAY DIFFRACTION99.66
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)
12.728077761230.7821836735350.2288057177655.46620305114-0.7665342154554.374659146710.0616468376052-0.7519033450811.181265295380.838641888916-0.0606436250558-0.326052956467-0.6377860526120.234005430670.3918188961990.171998903206-0.00494570911701-0.05157006315760.228343769393-0.3234897461580.61429932273710.246999262527.387668968644.4550208124
23.355596168110.3577863313160.5994110623642.614457175150.6593196470243.01123584844-0.2326950289460.850703077736-0.68557000859-0.2037799802870.270411053434-0.2957840052950.3430171458970.408704627822-0.1024267819590.122751370278-0.1081960250350.008259037724910.280275176671-0.3393467432780.31381960764114.358014363310.909870498829.4021669664
33.508562618510.5880173563250.06625700661243.019715018180.2573271566362.03345495676-0.245423639493-0.1318056984060.9830644654460.2687008237380.168031490369-0.059773275726-0.3089108127640.218653602893-0.007553862129770.0228552074138-0.0153313566827-0.05551585485050.22256328928-0.12642375970.4223321815917.262639519221.74616651637.953917947
45.332681183120.067081198310.5968629567416.66816100258-1.554162194634.09232725357-0.0678631817481.205415947890.1569878501-0.4949708190680.0347852956307-0.611678920945-0.3929272570610.601409737281-0.01477696929980.219400115561-0.1227915074410.1063448156960.496411648249-0.1532907349640.4909861879923.998597945416.418004039628.4043828863
53.140470383090.0984418182282-0.7134665216661.47395380544-0.08216402638372.743712015530.06442058770240.570407549366-0.0664963086394-0.2532947128620.0234870072548-0.145946520271-0.122008882155-0.1278473822470.1833799761490.181767051222-0.007653591877760.02046266054060.732936651107-0.1574336771130.13906719102728.749665442614.9786135748-12.1111577155
63.606953385480.5030077371391.997754552471.713615483640.7908696384964.129091787780.0158256530669-0.659620040463-0.1318623032050.2009113585990.06984904418640.01195592746860.112866908243-0.4050464388170.01383734639390.134791720901-0.00229874212678-0.03706452757930.6957290205080.02772824617510.035722940432332.730061875514.859461736510.3960265223
75.62722264777-1.041054327311.159526214742.616166940220.8379197187795.375205452980.01081591907340.773493633338-0.340376804902-0.422046226744-0.158238660107-0.1743766383220.01761807253240.610276617118-0.05770868836610.305910896764-0.01556651156210.01140096878190.857715477921-0.05269764519470.28016327276534.941732585915.3962786878-7.17795850428
82.669076587062.371201339152.647143138672.199845193422.775356837174.549145883130.5330830033660.628014157772-1.33198144308-0.1913136686120.003977887911270.18508251460.665871261846-0.0202928259119-0.5230749833820.2864130964340.0822361799156-0.1555260144420.678646732742-0.1509121665290.77695861731331.223990115.81012335245-4.7547753244
95.07243913760.5017229079182.904667043542.428864106350.3090381070175.84681555859-0.046552425301-0.4017272215930.1592826644690.1906672328550.022087935521-0.0439978752397-0.0307010517027-0.0277226752798-0.009481388165040.0686066316544-0.00706758297493-0.05841487132950.474784061101-0.09076939897630.11173847303839.284412618916.96527140747.50511456334
107.549288634720.005330956620431.780699922074.964951062411.169621036237.104358800890.3521842667060.494725703043-1.21317575565-0.2402739454260.0470800337985-0.1895893415630.7298882544160.571463767124-0.5329248070030.3384354805350.0662503304952-0.09998338398830.560618578032-0.07113592536230.40734460629343.17503748015.781359292483.10686105112
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 189 through 207 )AA189 - 2071 - 19
22chain 'A' and (resid 208 through 233 )AA208 - 23320 - 45
33chain 'A' and (resid 234 through 270 )AA234 - 27046 - 82
44chain 'A' and (resid 271 through 295 )AA271 - 29583 - 107
55chain 'B' and (resid 188 through 207 )BB188 - 2071 - 20
66chain 'B' and (resid 208 through 233 )BB208 - 23321 - 46
77chain 'B' and (resid 234 through 253 )BB234 - 25347 - 66
88chain 'B' and (resid 254 through 258 )BB254 - 25867 - 71
99chain 'B' and (resid 259 through 279 )BB259 - 27972 - 92
1010chain 'B' and (resid 280 through 295 )BB280 - 29593 - 108

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