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- PDB-8cnl: Lymphocytic choriomeningitis virus 3'-5' exonuclease domain of nu... -

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Basic information

Entry
Database: PDB / ID: 8cnl
TitleLymphocytic choriomeningitis virus 3'-5' exonuclease domain of nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / exonuclease / arenavirus / LCMV
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / viral nucleocapsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / RNA binding / metal ion binding
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain
Similarity search - Domain/homology
Biological speciesArenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSpiliopoulou, M. / Papageorgiou, N. / Ferron, F.
Funding support Greece, European Union, 2items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)3051 Greece
General Secretariat for Research and Technology (GSRT)European Union
CitationJournal: To Be Published
Title: Lymphocytic choriomeningitis virus 3'-5' exonuclease domain of nucleoprotein
Authors: Spiliopoulou, M. / Papageorgiou, N. / Ferron, F.
History
DepositionFeb 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nucleoprotein
A: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,69216
Polymers196,1698
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-51 kcal/mol
Surface area78230 Å2
Unit cell
Length a, b, c (Å)95.076, 95.066, 129.130
Angle α, β, γ (deg.)90.00, 97.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 24521.111 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arenavirus / Gene: N, Segment S / Production host: Escherichia phage T7 (virus)
References: UniProt: P09992, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.05M Sodium cacodylate pH 6.8, 0.01M Magnesium sulfate, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.8→94.254 Å / Num. obs: 310351 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.996 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
4.47-94.25413.4201290.9951
3.17-4.476.35366650.9821

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Processing

Software
NameClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→81.15 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2798 3891 3.54 %
Rwork0.2734 --
obs0.2736 109980 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→81.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12968 0 8 0 12976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113248
X-RAY DIFFRACTIONf_angle_d1.36817896
X-RAY DIFFRACTIONf_dihedral_angle_d19.3585056
X-RAY DIFFRACTIONf_chiral_restr0.0851952
X-RAY DIFFRACTIONf_plane_restr0.0072328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.830.51021360.4693749X-RAY DIFFRACTION99
2.83-2.870.45621420.45453838X-RAY DIFFRACTION100
2.87-2.910.60521330.4383715X-RAY DIFFRACTION100
2.91-2.950.36981400.39633773X-RAY DIFFRACTION100
2.95-2.990.40121400.38083827X-RAY DIFFRACTION100
2.99-3.030.3551400.37483744X-RAY DIFFRACTION100
3.03-3.080.37761380.36413806X-RAY DIFFRACTION100
3.08-3.130.34961350.35333765X-RAY DIFFRACTION99
3.13-3.190.37561390.35523805X-RAY DIFFRACTION99
3.19-3.240.33711400.35143726X-RAY DIFFRACTION100
3.24-3.310.34841420.33933801X-RAY DIFFRACTION100
3.31-3.370.39271410.31223805X-RAY DIFFRACTION100
3.37-3.450.3561360.29983749X-RAY DIFFRACTION100
3.45-3.530.32451410.28043856X-RAY DIFFRACTION100
3.53-3.620.30011380.28363776X-RAY DIFFRACTION100
3.62-3.710.25531390.27313794X-RAY DIFFRACTION100
3.71-3.820.30221380.27543837X-RAY DIFFRACTION100
3.82-3.950.32181420.27323799X-RAY DIFFRACTION100
3.95-4.090.26921400.24473775X-RAY DIFFRACTION100
4.09-4.250.18911380.24453792X-RAY DIFFRACTION100
4.25-4.440.20711400.24223819X-RAY DIFFRACTION100
4.44-4.680.2421430.22163775X-RAY DIFFRACTION100
4.68-4.970.23681380.2273832X-RAY DIFFRACTION100
4.97-5.360.28281420.24333790X-RAY DIFFRACTION100
5.36-5.890.27161380.24393823X-RAY DIFFRACTION100
5.89-6.750.27951380.27883792X-RAY DIFFRACTION100
6.75-8.50.19621400.22613799X-RAY DIFFRACTION100
8.5-81.150.16941340.18863727X-RAY DIFFRACTION98

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