+Open data
-Basic information
Entry | Database: PDB / ID: 3jb4 | ||||||
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Title | Structure of Ljungan virus: insight into picornavirus packaging | ||||||
Components |
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Keywords | VIRUS / picornaviruses / assembly / pathogen | ||||||
Function / homology | Function and homology information : / host cell nucleolus / host cell Golgi membrane / picornain 3C / host cell cytoplasmic vesicle membrane / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity ...: / host cell nucleolus / host cell Golgi membrane / picornain 3C / host cell cytoplasmic vesicle membrane / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / host cell endoplasmic reticulum membrane / symbiont entry into host cell / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Ljungan virus 87-012 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Zhu, L. / Wang, X.X. / Ren, J.S. / Porta, C. / Wenham, H. / Ekstrom, J.-O. / Panjwani, A. / Knowles, N.J. / Kotecha, A. / Siebert, A. ...Zhu, L. / Wang, X.X. / Ren, J.S. / Porta, C. / Wenham, H. / Ekstrom, J.-O. / Panjwani, A. / Knowles, N.J. / Kotecha, A. / Siebert, A. / Lindberg, M. / Fry, E.E. / Rao, Z.H. / Tuthill, T.J. / Stuart, D.I. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structure of Ljungan virus provides insight into genome packaging of this picornavirus. Authors: Ling Zhu / Xiangxi Wang / Jingshan Ren / Claudine Porta / Hannah Wenham / Jens-Ola Ekström / Anusha Panjwani / Nick J Knowles / Abhay Kotecha / C Alistair Siebert / A Michael Lindberg / ...Authors: Ling Zhu / Xiangxi Wang / Jingshan Ren / Claudine Porta / Hannah Wenham / Jens-Ola Ekström / Anusha Panjwani / Nick J Knowles / Abhay Kotecha / C Alistair Siebert / A Michael Lindberg / Elizabeth E Fry / Zihe Rao / Tobias J Tuthill / David I Stuart / Abstract: Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are ...Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans. The 3.78-Å resolution cryo-electron microscopy structure shows remarkable features, including an extended VP1 C terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N terminus of VP3, binding to which orders some 12% of the viral genome. This apparently charge-driven RNA attachment suggests that this branch of the picornaviruses uses a different mechanism of genome encapsidation, perhaps explored early in the evolution of picornaviruses. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jb4.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jb4.ent.gz | 113.8 KB | Display | PDB format |
PDBx/mmJSON format | 3jb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jb4_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3jb4_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3jb4_validation.xml.gz | 28 KB | Display | |
Data in CIF | 3jb4_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jb4 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jb4 | HTTPS FTP |
-Related structure data
Related structure data | 6394MC 6395C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 33091.980 Da / Num. of mol.: 1 / Fragment: UNP residues 504-800 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ljungan virus 87-012 / Cell line (production host): kidney (Vero) cell / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q8JV21 |
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#2: Protein | Mass: 28237.660 Da / Num. of mol.: 1 / Fragment: UNP residues 1-259 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ljungan virus 87-012 / Cell line (production host): kidney (Vero) cell / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q8JV21 |
#3: Protein | Mass: 27672.650 Da / Num. of mol.: 1 / Fragment: UNP residues 260-503 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ljungan virus 87-012 / Cell line (production host): kidney (Vero) cell / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q8JV21 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ljungan virus (type: 87-012) / Type: VIRUS |
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Molecular weight | Value: 6 MDa / Experimental value: YES |
Details of virus | Empty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Rodentia |
Buffer solution | Name: PBS / pH: 7.4 / Details: PBS |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Grids with adsorbed viruses were floated on 1% w/v uranyl acetate for 20 seconds. |
Specimen support | Details: 200 mesh gold grid with thin carbon support, glow-discharged in amylamine atmosphere |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % Details: Blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK III). Method: Blot for 3 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Feb 2, 2015 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2 mm Astigmatism: Objective lens astigmatism was corrected at 160,000 times magnification. |
Specimen holder | Specimen holder model: GATAN HELIUM |
Image recording | Film or detector model: GATAN K2 (4k x 4k) |
EM imaging optics | Energyfilter name: FEI |
Image scans | Num. digital images: 288 |
-Processing
EM software | Name: RELION / Category: 3D reconstruction | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5558 / Nominal pixel size: 1.35 Å / Actual pixel size: 1.35 Å / Details: (Single particle--Applied symmetry: I) / Num. of class averages: 20 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.8→129.6 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.962 / SU B: 18.956 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.426 / ESU R Free: 0.361 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.82 Å2 / Biso mean: 70.53 Å2 / Biso min: 9.93 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→129.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.8→3.899 Å / Total num. of bins used: 20
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