+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6394 | |||||||||
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Title | Structure of Ljungan virus: insight into picornavirus packaging | |||||||||
Map data | Reconstruction of Ljungan virus at 3.8 Angstrom resolution | |||||||||
Sample |
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Keywords | Ljungan virus / Picornavirus / 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 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.8 Å | |||||||||
Authors | Zhu L / Wang XX / Ren JS / Porta C / Wenham H / Ekstrom J-O / Panjwani A / Knowles NJ / Kotecha A / Siebert A ...Zhu L / Wang XX / Ren JS / Porta C / Wenham H / Ekstrom J-O / Panjwani A / Knowles NJ / Kotecha A / Siebert A / Lindberg M / Fry EE / Rao ZH / Tuthill TJ / Stuart DI | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6394.map.gz | 166.1 MB | EMDB map data format | |
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Header (meta data) | emd-6394-v30.xml emd-6394.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_6394.tif | 265 KB | ||
Masks | emd_6394_msk_1.map | 178 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6394 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6394 | HTTPS FTP |
-Validation report
Summary document | emd_6394_validation.pdf.gz | 475.4 KB | Display | EMDB validaton report |
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Full document | emd_6394_full_validation.pdf.gz | 474.9 KB | Display | |
Data in XML | emd_6394_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6394 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6394 | HTTPS FTP |
-Related structure data
Related structure data | 3jb4MC 6395C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6394.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Ljungan virus at 3.8 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: This mask is used to 3D-Autorefinement
Annotation | This mask is used to 3D-Autorefinement | ||||||||||||
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File | emd_6394_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ljungan virus (type: 87-012)
Entire | Name: Ljungan virus (type: 87-012) |
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Components |
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-Supramolecule #1000: Ljungan virus (type: 87-012)
Supramolecule | Name: Ljungan virus (type: 87-012) / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 6 MDa / Theoretical: 6 MDa / Method: Sedimentation |
-Supramolecule #1: Ljungan virus
Supramolecule | Name: Ljungan virus / type: virus / ID: 1 / NCBI-ID: 172314 / Sci species name: Ljungan virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Mus sp. (mice) / synonym: VERTEBRATES |
Host system | Organism: Chlorocebus aethiops (grivet) / Recombinant cell: green monkey kidney (Vero) cells |
Molecular weight | Experimental: 6 MDa / Theoretical: 6 MDa |
Virus shell | Shell ID: 1 / Diameter: 320 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 / Details: PBS |
Staining | Type: NEGATIVE Details: Grids with adsorbed viruses were floated on 1% w/v uranyl acetate for 20 seconds. |
Grid | Details: 200 mesh gold grid with thin carbon support, glow-discharged in amylamine atmosphere |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 3 seconds before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 160,000 times magnification. |
Specialist optics | Energy filter - Name: FEI |
Date | Feb 2, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 288 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm |
Sample stage | Specimen holder model: GATAN HELIUM |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 5558 |
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Final two d classification | Number classes: 20 |