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Yorodumi- EMDB-2389: The limits of structural plasticity in a picornavirus capsid reve... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2389 | |||||||||
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Title | The limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle | |||||||||
Map data | Reconstruction of native equine rhinitis A virus | |||||||||
Sample |
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Keywords | virus / picornavirus / capsid structure / capsid expansion / uncoating | |||||||||
Function / homology | Function and homology information icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Equine rhinitis A virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
Authors | Bakker SE / Groppelli E / Pearson AR / Stockley PG / Rowlands DJ / Ranson NA | |||||||||
Citation | Journal: J Virol / Year: 2014 Title: Limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle. Authors: Saskia E Bakker / Elisabetta Groppelli / Arwen R Pearson / Peter G Stockley / David J Rowlands / Neil A Ranson / Abstract: The Picornaviridae family of small, nonenveloped viruses includes major pathogens of humans and animals. They have positive-sense, single-stranded RNA genomes, and the mechanism(s) by which these ...The Picornaviridae family of small, nonenveloped viruses includes major pathogens of humans and animals. They have positive-sense, single-stranded RNA genomes, and the mechanism(s) by which these genomes are introduced into cells to initiate infection remains poorly understood. The structures of presumed uncoating intermediate particles of several picornaviruses show limited expansion and some increased porosity compared to the mature virions. Here, we present the cryo-electron microscopy structure of native equine rhinitis A virus (ERAV), together with the structure of a massively expanded ERAV particle, each at ∼17-Å resolution. The expanded structure has large pores on the particle 3-fold axes and has lost the RNA genome and the capsid protein VP4. The expanded structure thus illustrates both the limits of structural plasticity in such capsids and a plausible route by which genomic RNA might exit. IMPORTANCE: Picornaviruses are important animal and human pathogens that protect their genomic RNAs within a protective protein capsid. Upon infection, this genomic RNA must be able to leave the ...IMPORTANCE: Picornaviruses are important animal and human pathogens that protect their genomic RNAs within a protective protein capsid. Upon infection, this genomic RNA must be able to leave the capsid to initiate a new round of infection. We describe here the structure of a unique, massively expanded state of equine rhinitis A virus that provides insight into how this exit might occur. | |||||||||
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_2389.map.gz | 13.5 MB | EMDB map data format | |
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Header (meta data) | emd-2389-v30.xml emd-2389.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_2389.png | 186 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2389 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2389 | HTTPS FTP |
-Validation report
Summary document | emd_2389_validation.pdf.gz | 234.1 KB | Display | EMDB validaton report |
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Full document | emd_2389_full_validation.pdf.gz | 233.2 KB | Display | |
Data in XML | emd_2389_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2389 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2389 | HTTPS FTP |
-Related structure data
Related structure data | 4ctfMC 2390C 4ctgC 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_2389.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of native equine rhinitis A virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.72 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : native equine rhinitis A virus
Entire | Name: native equine rhinitis A virus |
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Components |
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-Supramolecule #1000: native equine rhinitis A virus
Supramolecule | Name: native equine rhinitis A virus / type: sample / ID: 1000 / Oligomeric state: One icosahedral virus particle / Number unique components: 1 |
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-Supramolecule #1: Equine rhinitis A virus
Supramolecule | Name: Equine rhinitis A virus / type: virus / ID: 1 / Name.synonym: ERAV / NCBI-ID: 47000 / Sci species name: Equine rhinitis A virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: ERAV |
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Host (natural) | Organism: Equus caballus (horse) / synonym: VERTEBRATES |
Host system | Organism: Homo sapiens (human) / Recombinant cell: HeLa cells |
Virus shell | Shell ID: 1 / Diameter: 316 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Grid | Details: 300 mesh quantifoil R1.2/1.3 grids, glow discharged in air. |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Jan 1, 2011 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 87209 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm |
Sample stage | Specimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: phase flipping, each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 260 |
Final two d classification | Number classes: 78 |