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Yorodumi- EMDB-6223: Subtomogram averaging of the empty tube of lemon-shaped archaeal ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6223 | |||||||||
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Title | Subtomogram averaging of the empty tube of lemon-shaped archaeal virus His1 | |||||||||
Map data | Subtomogram average of empty tube of archaeal virus His1 from all-vs-all | |||||||||
Sample |
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Keywords | Lemon-shaped Virus / Tail Organization / Electron Cryo-Tomography / Subtomogram averaging / Dissociation | |||||||||
Biological species | Lemon-shaped archaeal virus His1 | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
Authors | Hong C / Pietila MK / Fu C / Schmid MF / Bamford DH / Chiu W | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Lemon-shaped halo archaeal virus His1 with uniform tail but variable capsid structure. Authors: Chuan Hong / Maija K Pietilä / Caroline J Fu / Michael F Schmid / Dennis H Bamford / Wah Chiu / Abstract: Lemon-shaped viruses are common in nature but so far have been observed to infect only archaea. Due to their unusual shape, the structures of these viruses are challenging to study and therefore ...Lemon-shaped viruses are common in nature but so far have been observed to infect only archaea. Due to their unusual shape, the structures of these viruses are challenging to study and therefore poorly characterized. Here, we have studied haloarchaeal virus His1 using cryo-electron tomography as well as biochemical dissociation. The virions have different sizes, but prove to be extremely stable under various biochemical treatments. Subtomogram averaging of the computationally extracted virions resolved a tail-like structure with a central tail hub density and six tail spikes. Inside the tail there are two cavities and a plug density that separates the tail hub from the interior genome. His1 most likely uses the tail spikes to anchor to host cells and the tail hub to eject the genome, analogous to classic tailed bacteriophages. Upon biochemical treatment that releases the genome, the lemon-shaped virion transforms into an empty tube. Such a dramatic transformation demonstrates that the capsid proteins are capable of undergoing substantial quaternary structural changes, which may occur at different stages of the virus life cycle. | |||||||||
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_6223.map.gz | 384.7 MB | EMDB map data format | |
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Header (meta data) | emd-6223-v30.xml emd-6223.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | 400_6223.gif 80_6223.gif | 21.1 KB 1.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6223 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6223 | HTTPS FTP |
-Validation report
Summary document | emd_6223_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_6223_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_6223_validation.xml.gz | 499 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6223 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6223 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6223.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram average of empty tube of archaeal virus His1 from all-vs-all | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.52 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 : Empty tube of lemon-shaped archaeal virus His1
Entire | Name: Empty tube of lemon-shaped archaeal virus His1 |
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Components |
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-Supramolecule #1000: Empty tube of lemon-shaped archaeal virus His1
Supramolecule | Name: Empty tube of lemon-shaped archaeal virus His1 / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Lemon-shaped archaeal virus His1
Supramolecule | Name: Lemon-shaped archaeal virus His1 / type: virus / ID: 1 / Details: Heat-induced empty tube / Sci species name: Lemon-shaped archaeal virus His1 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Haloarcula hispanica (Halophile) / synonym: ARCHAEA |
Virus shell | Shell ID: 1 / Diameter: 220 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 Details: 50 mM NaCl, 3.5 mM MgCl2, 1 mM KCl, 0.1 mM CaCl2, 50 mM Tris-HCl, pH 7.2 |
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Grid | Details: 200 mesh Quantifoil grids, glow discharged for 15 seconds |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 2 seconds |
-Electron microscopy
Microscope | JEOL 2200FS |
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Temperature | Min: 80 K / Max: 93 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Corrected at 100,000x magnification |
Specialist optics | Energy filter - Name: Omega JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Oct 1, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 200 / Average electron dose: 100 e/Å2 / Camera length: 150 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 33186 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 25000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 ° |
-Image processing
Details | All-vs-all classification |
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Final reconstruction | Algorithm: OTHER / Software - Name: IMOD, EMAN, EMAN2, tomohunter / Number subtomograms used: 54 |