+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6310 | |||||||||
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Title | A Virus that Infects a Hyperthermophile Encapsidates A-Form DNA | |||||||||
Map data | Reconstruction of SIRV2 | |||||||||
Sample |
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Keywords | archaeal virus / helical symmetry | |||||||||
Function / homology | Sulfolobus virus, coat protein, C-terminal / Sulfolobus virus coat protein C terminal / helical viral capsid / DNA binding / Major capsid protein Function and homology information | |||||||||
Biological species | Sulfolobus islandicus rod-shaped virus 2 | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | DiMaio F / Yu X / Rensen E / Krupovic M / Prangishvili D / Egelman E | |||||||||
Citation | Journal: Science / Year: 2015 Title: Virology. A virus that infects a hyperthermophile encapsidates A-form DNA. Authors: Frank DiMaio / Xiong Yu / Elena Rensen / Mart Krupovic / David Prangishvili / Edward H Egelman / Abstract: Extremophiles, microorganisms thriving in extreme environmental conditions, must have proteins and nucleic acids that are stable at extremes of temperature and pH. The nonenveloped, rod-shaped virus ...Extremophiles, microorganisms thriving in extreme environmental conditions, must have proteins and nucleic acids that are stable at extremes of temperature and pH. The nonenveloped, rod-shaped virus SIRV2 (Sulfolobus islandicus rod-shaped virus 2) infects the hyperthermophilic acidophile Sulfolobus islandicus, which lives at 80°C and pH 3. We have used cryo-electron microscopy to generate a three-dimensional reconstruction of the SIRV2 virion at ~4 angstrom resolution, which revealed a previously unknown form of virion organization. Although almost half of the capsid protein is unstructured in solution, this unstructured region folds in the virion into a single extended α helix that wraps around the DNA. The DNA is entirely in the A-form, which suggests a common mechanism with bacterial spores for protecting DNA in the most adverse environments. | |||||||||
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_6310.map.gz | 29.4 MB | EMDB map data format | |
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Header (meta data) | emd-6310-v30.xml emd-6310.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | 400_6310.gif 80_6310.gif | 76.7 KB 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6310 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6310 | HTTPS FTP |
-Validation report
Summary document | emd_6310_validation.pdf.gz | 383.9 KB | Display | EMDB validaton report |
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Full document | emd_6310_full_validation.pdf.gz | 383.4 KB | Display | |
Data in XML | emd_6310_validation.xml.gz | 4.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6310 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6310 | HTTPS FTP |
-Related structure data
Related structure data | 3j9xMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10060 (Title: Subset of image stack used for 3D reconstruction / Data size: 35.9 Data #1: image segments of SIRV2 [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6310.map.gz / Format: CCP4 / Size: 31.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of SIRV2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 : SIRV2
Entire | Name: SIRV2 |
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Components |
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-Supramolecule #1000: SIRV2
Supramolecule | Name: SIRV2 / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Sulfolobus islandicus rod-shaped virus 2
Supramolecule | Name: Sulfolobus islandicus rod-shaped virus 2 / type: virus / ID: 1 / Name.synonym: SIRV2 / NCBI-ID: 157899 / Sci species name: Sulfolobus islandicus rod-shaped virus 2 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: SIRV2 |
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Host (natural) | Organism: Sulfolobus islandicus (acidophilic) / synonym: ARCHAEA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Sep 19, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 437 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | IHRSR |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 2.9 Å Applied symmetry - Helical parameters - Δ&Phi: 24.5 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: Spider |
CTF correction | Details: multiply images by CTF, divide reconstruction by sum of CTF**2 |