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- PDB-8cjw: Nucleoprotein Thogotovirus delta188-196 -

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Basic information

Entry
Database: PDB / ID: 8cjw
TitleNucleoprotein Thogotovirus delta188-196
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / viral replication / nucleoprotein / RNA binding / orthomyxovirus
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / RNA binding
Similarity search - Function
PHOSPHATE ION / SUCCINIC ACID / Nucleoprotein
Similarity search - Component
Biological speciesThogotovirus thogotoense
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsDick, A. / Roske, Y.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DA 1127/1-2 and SFB958/A12 Germany
CitationJournal: Structure / Year: 2024
Title: Structural characterization of Thogoto Virus nucleoprotein provides insights into viral RNA encapsidation and RNP assembly.
Authors: Alexej Dick / Vasilii Mikirtumov / Jonas Fuchs / Ferdinand Krupp / Daniel Olal / Elias Bendl / Thiemo Sprink / Christoph Diebolder / Mikhail Kudryashev / Georg Kochs / Yvette Roske / Oliver Daumke /
Abstract: Orthomyxoviruses, such as influenza and thogotoviruses, are important human and animal pathogens. Their segmented viral RNA genomes are wrapped by viral nucleoproteins (NPs) into helical ...Orthomyxoviruses, such as influenza and thogotoviruses, are important human and animal pathogens. Their segmented viral RNA genomes are wrapped by viral nucleoproteins (NPs) into helical ribonucleoprotein complexes (RNPs). NP structures of several influenza viruses have been reported. However, there are still contradictory models of how orthomyxovirus RNPs are assembled. Here, we characterize the crystal structure of Thogoto virus (THOV) NP and found striking similarities to structures of influenza viral NPs, including a two-lobed domain architecture, a positively charged RNA-binding cleft, and a tail loop important for trimerization and viral transcription. A low-resolution cryo-electron tomography reconstruction of THOV RNPs elucidates a left-handed double helical assembly. By providing a model for RNP assembly of THOV, our study suggests conserved NP assembly and RNA encapsidation modes for thogoto- and influenza viruses.
History
DepositionFeb 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3667
Polymers49,8721
Non-polymers4946
Water3,765209
1
A: Nucleoprotein
hetero molecules

A: Nucleoprotein
hetero molecules

A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,09921
Polymers149,6173
Non-polymers1,48318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area15460 Å2
ΔGint-67 kcal/mol
Surface area54060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.110, 119.110, 91.638
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 49872.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: internal deletion of residues 188-196 / Source: (gene. exp.) Thogotovirus thogotoense / Gene: Segment 5 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P89216
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 21% PEG 1500, 0.1M SPG pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9814, 0.97973
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98141
20.979731
ReflectionResolution: 2.01→44.9 Å / Num. obs: 32179 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 59.79 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.056 / Net I/σ(I): 15.3
Reflection shellResolution: 2.01→2.13 Å / Redundancy: 4.2 % / Num. unique obs: 5199 / CC1/2: 0.329 / Rrim(I) all: 0.1975 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→41.874 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 34.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1608 5 %
Rwork0.1846 --
obs0.187 32135 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→41.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 30 209 3621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083531
X-RAY DIFFRACTIONf_angle_d0.8964767
X-RAY DIFFRACTIONf_dihedral_angle_d4.32950
X-RAY DIFFRACTIONf_chiral_restr0.057505
X-RAY DIFFRACTIONf_plane_restr0.007610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.07340.56641430.54032733X-RAY DIFFRACTION98
2.0734-2.14750.48981480.44492812X-RAY DIFFRACTION99
2.1475-2.23350.40041480.35482790X-RAY DIFFRACTION100
2.2335-2.33520.35441460.28872766X-RAY DIFFRACTION99
2.3352-2.45830.31751450.26482757X-RAY DIFFRACTION100
2.4583-2.61230.31611470.25172787X-RAY DIFFRACTION99
2.6123-2.81390.29021460.21622774X-RAY DIFFRACTION100
2.8139-3.0970.28651450.21582767X-RAY DIFFRACTION99
3.097-3.5450.23691480.17892801X-RAY DIFFRACTION99
3.545-4.46550.18311450.14792769X-RAY DIFFRACTION100
4.4655-41.8740.18761470.14332771X-RAY DIFFRACTION99
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)
14.4066-0.1589-0.43312.4096-0.32171.89440.27070.192-0.4461-0.044-0.2072-0.23580.03560.4763-0.05980.41640.0577-0.14790.4501-0.05590.4917-25.441-17.42710.8105
23.93771.255-0.22351.1097-0.30250.95940.21920.6911-0.9285-0.2485-0.07220.02140.35330.1871-0.10590.65880.1613-0.21850.5804-0.21220.6508-39.3547-23.5139-8.6724
33.04751.01880.9905-0.66930.62510.11150.13590.0662-0.34270.1302-0.03940.01280.1675-0.1387-0.05480.60890.0569-0.01780.4527-0.07920.9701-58.2108-22.73150.0845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 310 )
2X-RAY DIFFRACTION2chain 'A' and (resid 311 through 378 )
3X-RAY DIFFRACTION3chain 'A' and (resid 379 through 454 )

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