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- PDB-8u0a: Crystal structure of Lyssavirus rabies (Ni-CE strain) nucleoprote... -

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Basic information

Entry
Database: PDB / ID: 8u0a
TitleCrystal structure of Lyssavirus rabies (Ni-CE strain) nucleoprotein in complex with phosphoprotein chaperone
ComponentsPhosphoprotein, Nucleoprotein fusion
KeywordsVIRAL PROTEIN / nucleoprotein / phosphoprotein / chaperone
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / 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 / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral nucleocapsid / symbiont-mediated suppression of host toll-like receptor signaling pathway ...microtubule-dependent intracellular transport of viral material towards nucleus / 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 / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral nucleocapsid / 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 / ribonucleoprotein complex / RNA-directed RNA polymerase activity / host cell nucleus / RNA binding
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
Nucleoprotein / Phosphoprotein
Similarity search - Component
Biological speciesRabies virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDonnelly, C.M. / Stewart, M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Lyssavirus rabies (Ni-CE strain) nucleoprotein in complex with phosphoprotein chaperone
Authors: Donnelly, C.M. / Stewart, M. / Forwood, J.K.
History
DepositionAug 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoprotein, Nucleoprotein fusion


Theoretical massNumber of molelcules
Total (without water)58,3821
Polymers58,3821
Non-polymers00
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.170, 74.496, 154.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoprotein, Nucleoprotein fusion


Mass: 58381.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies virus (strain Nishigahara RCEH) / Strain: Ni-CE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9IPJ8, UniProt: O55611
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 0.2 M magnesium acetate tetrahydrate 20% polyethylene glycol 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 EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→29.9 Å / Num. obs: 33852 / % possible obs: 98.1 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.38 / Num. unique obs: 2309 / CC1/2: 0.656 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.9 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1719 5.2 %
Rwork0.1822 --
obs0.184 33041 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3239 0 0 384 3623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063337
X-RAY DIFFRACTIONf_angle_d0.7284515
X-RAY DIFFRACTIONf_dihedral_angle_d12.1351222
X-RAY DIFFRACTIONf_chiral_restr0.046494
X-RAY DIFFRACTIONf_plane_restr0.007585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.33271350.26842456X-RAY DIFFRACTION94
2.06-2.130.28881440.27812460X-RAY DIFFRACTION93
2.13-2.20.27741220.20582545X-RAY DIFFRACTION96
2.2-2.290.26461310.22582478X-RAY DIFFRACTION95
2.29-2.390.21511280.18282576X-RAY DIFFRACTION97
2.39-2.520.25791780.1792553X-RAY DIFFRACTION98
2.52-2.680.22631530.17252646X-RAY DIFFRACTION100
2.68-2.880.19031220.17852663X-RAY DIFFRACTION100
2.88-3.170.23891450.17792681X-RAY DIFFRACTION100
3.17-3.630.21521370.16782691X-RAY DIFFRACTION100
3.63-4.570.17411470.14722725X-RAY DIFFRACTION100
4.57-29.90.18961770.18622848X-RAY DIFFRACTION100
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)
11.6836-1.12-1.96611.78181.84443.56920.21570.4844-0.0351-0.5561-0.21540.0925-0.4017-0.3180.01110.32620.0169-0.03620.24930.06560.283726.581947.696519.73
21.43190.07530.50061.55-0.42042.5897-0.0005-0.0543-0.07060.042-0.0008-0.09430.11640.16250.0030.09710.0094-0.00610.1166-0.00820.15531.333145.355648.2145
31.3034-1.4938-1.06552.43361.77211.96490.11260.2707-0.0197-0.4087-0.17530.1338-0.2574-0.13650.07740.20930.0044-0.04640.1840.00170.148929.176940.47718.5169
42.6128-0.86010.75332.1748-1.16614.66040.09380.3417-0.0359-0.3092-0.1874-0.0697-0.23440.22440.09910.24360.03340.00970.2128-0.01350.177238.970227.61417.4031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 290 )
3X-RAY DIFFRACTION3chain 'A' and (resid 291 through 393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 508 )

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