+Open data
-Basic information
Entry | Database: PDB / ID: 8cjw | ||||||
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Title | Nucleoprotein Thogotovirus delta188-196 | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL 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 / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Thogotovirus thogotoense | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å | ||||||
Authors | Dick, A. / Roske, Y. | ||||||
Funding support | Germany, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cjw.cif.gz | 194.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cjw.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 8cjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cjw_validation.pdf.gz | 456.9 KB | Display | wwPDB validaton report |
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Full document | 8cjw_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 8cjw_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 8cjw_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/8cjw ftp://data.pdbj.org/pub/pdb/validation_reports/cj/8cjw | HTTPS FTP |
-Related structure data
Related structure data | 8rytC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | ||||||
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#2: Chemical | ChemComp-SIN / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 21% PEG 1500, 0.1M SPG pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9814, 0.97973 | |||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2020 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→41.874 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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