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Yorodumi- EMDB-5427: Cryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5427 | |||||||||
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Title | Cryo-EM reconstruction of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation | |||||||||
Map data | Reconstruction of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation | |||||||||
Sample |
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Keywords | Time-resolved / T=4 / quasi-equivalence / maturation | |||||||||
Biological species | Nudaurelia capensis omega virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.6 Å | |||||||||
Authors | Matsui T / Lander GC / Khayat R / Johnson JE | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2010 Title: Subunits fold at position-dependent rates during maturation of a eukaryotic RNA virus. Authors: Tsutomu Matsui / Gabriel C Lander / Reza Khayat / John E Johnson / Abstract: Effective antiviral agents are difficult to develop because of the close relationship between the cell biology of the virus and host. However, viral capsid maturation, the in vivo process where the ...Effective antiviral agents are difficult to develop because of the close relationship between the cell biology of the virus and host. However, viral capsid maturation, the in vivo process where the particle transitions from a noninfectious provirion to an infectious virion, is an ideal process to interrupt because the provirion is usually fragile and the conversion to the virion often involves large conformational changes and autocatalytic chemistry that can be hampered by small molecules. The Nudaurelia capensis omega virus (N omegaV) is one of the few eukaryotic viruses where this process can be investigated in vitro with a variety of biophysical methods, allowing fundamental chemical and structural principles of the maturation to be established. It has a T = 4 quasi-equivalent capsid with a dramatic maturation pathway that includes a particle size reduction of 100 A and an autocatalytic cleavage. Here we use cryo-EM and difference maps, computed at three time points following maturation initiation, to show that regions of N omegaV subunit folding are maturation dependent and occur at rates determined by their quasi-equivalent position in the capsid, explaining the unusual kinetics of the maturation cleavage. This study shows that folding is rapid and peptide chain self-cleavage occurs early for subunits adjacent to 3-fold and 5-fold icosahedral symmetry elements and that folding is slower in regions where molecular switches are required for the formation of the proper interfacial contacts. The results connect viral maturation to the well-studied assembly-dependent folding that occurs in the formation of cellular complexes. | |||||||||
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_5427.map.gz | 12.5 MB | EMDB map data format | |
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Header (meta data) | emd-5427-v30.xml emd-5427.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | emd_5427_1.png | 159.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5427 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5427 | HTTPS FTP |
-Validation report
Summary document | emd_5427_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_5427_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_5427_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5427 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5427 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5427.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.768 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 : Nudaurelia capensis omega virus (NwV) capsid at 30min time point ...
Entire | Name: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation |
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Components |
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-Supramolecule #1000: Nudaurelia capensis omega virus (NwV) capsid at 30min time point ...
Supramolecule | Name: Nudaurelia capensis omega virus (NwV) capsid at 30min time point following maturation initiation type: sample / ID: 1000 / Oligomeric state: Icosahedral virus / Number unique components: 1 |
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-Supramolecule #1: Nudaurelia capensis omega virus
Supramolecule | Name: Nudaurelia capensis omega virus / type: virus / ID: 1 / Name.synonym: NwV (N omega V) / NCBI-ID: 12541 / Sci species name: Nudaurelia capensis omega virus / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: NwV (N omega V) |
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Host (natural) | Organism: Lepidoptera (butterflies and moths) / synonym: INVERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 400 Å / T number (triangulation number): 4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 5 / Details: 100mM NaOAc, 250mM NaCl |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 7sec before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Feb 13, 2008 |
Image recording | Number real images: 497 / Average electron dose: 16.5 e/Å2 Details: Data were collected using the Leginon automated electron microscopy package and data processing was performed using the Appion pipeline. |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each image |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN Details: Data processing was performed using the Appion pipeline. Number images used: 17174 |