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- PDB-8fwl: Crystal structure of Australian bat lyssavirus nucleoprotein in c... -

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Basic information

Entry
Database: PDB / ID: 8fwl
TitleCrystal structure of Australian bat lyssavirus nucleoprotein in complex with phosphoprotein chaperone
ComponentsPhosphoprotein,Nucleoprotein
KeywordsVIRAL PROTEIN / Chaperone / lyssavirus / nucleoprotein / phosphoprotein / rabies
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 innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex ...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 innate immune response / 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 australis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsDonnelly, C.M. / Stewart, M. / Forwood, J.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
Not funded Australia
CitationJournal: Viruses / Year: 2023
Title: Structural Determination of the Australian Bat Lyssavirus Nucleoprotein and Phosphoprotein Complex.
Authors: Donnelly, C.M. / Stewart, M. / Roby, J.A. / Sundaramoorthy, V. / Forwood, J.K.
History
DepositionJan 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoprotein,Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9022
Polymers63,7951
Non-polymers1061
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.373, 35.503, 89.091
Angle α, β, γ (deg.)90.00, 92.63, 90.00
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 63795.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus australis / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7M4C440, UniProt: Q9YZ24
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.12M Alcohol mix (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 1.0M Tris (base); BICINE,60% Precipitant Mix (40% ...Details: 0.12M Alcohol mix (0.2M 1,6-Hexanediol; 0.2M 1-Butanol; 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol), 1.0M Tris (base); BICINE,60% Precipitant Mix (40% v/v PEG 500* MME; 20 % w/v PEG 20000)

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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 26, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.19→29.67 Å / Num. obs: 26863 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.89 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.4
Reflection shellResolution: 2.19→2.26 Å / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2185 / CC1/2: 0.866 / Rpim(I) all: 0.268 / Rrim(I) all: 0.538

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→29.67 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 1371 5.1 %
Rwork0.1594 --
obs0.1611 26858 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 7 168 3435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043395
X-RAY DIFFRACTIONf_angle_d0.5464596
X-RAY DIFFRACTIONf_dihedral_angle_d13.2171247
X-RAY DIFFRACTIONf_chiral_restr0.04503
X-RAY DIFFRACTIONf_plane_restr0.005595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.270.22771430.20282390X-RAY DIFFRACTION96
2.27-2.360.19411550.16562554X-RAY DIFFRACTION100
2.36-2.470.2111510.16452479X-RAY DIFFRACTION100
2.47-2.60.19011300.15792529X-RAY DIFFRACTION100
2.6-2.760.19861440.16142549X-RAY DIFFRACTION100
2.76-2.980.2186990.17322585X-RAY DIFFRACTION100
2.98-3.280.20451260.17112558X-RAY DIFFRACTION100
3.28-3.750.20451470.16372563X-RAY DIFFRACTION100
3.75-4.720.16361410.13612584X-RAY DIFFRACTION100
4.72-29.670.18441350.15612696X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined3.39970.58912.62810.58450.56512.06110.0903-0.72570.26820.4916-0.21460.7912-0.022-1.21950.18830.38410.01250.15281.2419-0.01750.69727.302312.930916.2828
2refined2.4491-0.1162-0.22471.1183-0.0812.75430.03540.16230.1109-0.04220.0085-0.15430.06130.26440.00650.211-0.00060.01390.10160.02580.228550.341713.274527.2734
3refined21.02377.216710.2609
41.16530.65531.26941.08810.98283.04430.1011-0.0933-0.0445-0.087-0.10450.10490.3693-0.9157-0.00050.2418-0.0687-0.00840.47680.06950.2558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 375 )
3X-RAY DIFFRACTION3chain 'A' and (resid 376 through 591 )

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