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Yorodumi- EMDB-3097: Structure and genome release mechanism of human cardiovirus Saffo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3097 | |||||||||
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Title | Structure and genome release mechanism of human cardiovirus Saffold virus-3 | |||||||||
Map data | Reconstruction of the human cardiovirus Saffold virus-3 A particle | |||||||||
Sample |
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Keywords | Saffold / virus / cardiovirus / Picornavirales / A / altered / virion / particle / capsid / genome / RNA / ssRNA | |||||||||
Function / homology | Function and homology information RNA-protein covalent cross-linking / : / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization ...RNA-protein covalent cross-linking / : / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Human saffold virus-3 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 10.6 Å | |||||||||
Authors | Mullapudi E / Novacek J / Palkova L / Kulich P / Lindberg M / van Kuppeveld FJM / Plevka P | |||||||||
Citation | Journal: J Virol / Year: 2016 Title: Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3. Authors: Edukondalu Mullapudi / Jiří Nováček / Lenka Pálková / Pavel Kulich / A Michael Lindberg / Frank J M van Kuppeveld / Pavel Plevka / Abstract: In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not ...In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the uncoating of the nonenveloped human cardiovirus Saffold virus 3 (SAFV-3) of the family Picornaviridae SAFVs cause diseases ranging from gastrointestinal disorders to meningitis. We present a structure of a native SAFV-3 virion determined to 2.5 Å by X-ray crystallography and an 11-Å-resolution cryo-electron microscopy reconstruction of an "altered" particle that is primed for genome release. The altered particles are expanded relative to the native virus and contain pores in the capsid that might serve as channels for the release of VP4 subunits, N termini of VP1, and the RNA genome. Unlike in the related enteroviruses, pores in SAFV-3 are located roughly between the icosahedral 3- and 5-fold axes at an interface formed by two VP1 and one VP3 subunit. Furthermore, in native conditions many cardioviruses contain a disulfide bond formed by cysteines that are separated by just one residue. The disulfide bond is located in a surface loop of VP3. We determined the structure of the SAFV-3 virion in which the disulfide bonds are reduced. Disruption of the bond had minimal effect on the structure of the loop, but it increased the stability and decreased the infectivity of the virus. Therefore, compounds specifically disrupting or binding to the disulfide bond might limit SAFV infection. IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from ...IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from the capsid in order to initiate infection. This process is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the genome release of Human Saffold virus 3 Saffold viruses cause diseases ranging from gastrointestinal disorders to meningitis. We show that before the genome is released, the Saffold virus 3 particle expands, and holes form in the previously compact capsid. These holes serve as channels for the release of the genome and small capsid proteins VP4 that in related enteroviruses facilitate subsequent transport of the virus genome into the cell cytoplasm. | |||||||||
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_3097.map.gz | 116.5 MB | EMDB map data format | |
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Header (meta data) | emd-3097-v30.xml emd-3097.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | safv3-overview.png | 341.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3097 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3097 | HTTPS FTP |
-Related structure data
Related structure data | 5a8fMC 5cfcC 5cfdC 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_3097.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the human cardiovirus Saffold virus-3 A particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2176 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 : A particle of Saffold virus-3
Entire | Name: A particle of Saffold virus-3 |
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Components |
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-Supramolecule #1000: A particle of Saffold virus-3
Supramolecule | Name: A particle of Saffold virus-3 / type: sample / ID: 1000 / Details: The sample is monodisperse / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 5 MDa |
-Supramolecule #1: Human saffold virus-3
Supramolecule | Name: Human saffold virus-3 / type: virus / ID: 1 / Sci species name: Human saffold virus-3 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Theoretical: 5 MDa |
Virus shell | Shell ID: 1 / Diameter: 320 Å / T number (triangulation number): 3 |
Virus shell | Shell ID: 2 / Diameter: 320 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.5 / Details: 20mM Hepes, 150mM NaCl |
Staining | Type: NEGATIVE / Details: 0.5% molybdenum acetate for 30 seconds |
Grid | Details: 400 mesh Cu grid with thin carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: -3.95 µm / Nominal defocus min: -2.33 µm / Nominal magnification: 55000 |
Sample stage | Specimen holder: nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 62k magnification |
Date | Sep 3, 2014 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 3 µm / Number real images: 264 / Average electron dose: 20 e/Å2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.6 Å / Resolution method: OTHER / Software - Name: EMAN2, j3dr, jalign, Bsoft / Number images used: 14028 |
Details | EMAN2, jalign, j3dr programs used for particle selection and electron density map reconstruction |