+Open data
-Basic information
Entry | Database: PDB / ID: 3j9x | ||||||
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Title | A Virus that Infects a Hyperthermophile Encapsidates A-Form DNA | ||||||
Components |
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Keywords | VIRUS / archaeal virus / helical symmetry | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus islandicus rod-shaped virus 2 | ||||||
Method | ELECTRON MICROSCOPY / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j9x.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3j9x.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 3j9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j9x_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3j9x_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3j9x_validation.xml.gz | 154.1 KB | Display | |
Data in CIF | 3j9x_validation.cif.gz | 239 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/3j9x ftp://data.pdbj.org/pub/pdb/validation_reports/j9/3j9x | HTTPS FTP |
-Related structure data
Related structure data | 6310MC M: map data used to model this data 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
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 30 / Rise per n subunits: 2.9 Å / Rotation per n subunits: 24.5 °) |
Details | The helical parameters generate the capsid filament from chains A and B. |
-Components
#1: Protein | Mass: 13760.465 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Source: (natural) Sulfolobus islandicus rod-shaped virus 2 / References: UniProt: Q8V9P2 #2: DNA chain | Mass: 107382.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus islandicus rod-shaped virus 2 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Sulfolobus islandicus rod-shaped virus 2 / Type: VIRUS / Synonym: SIRV2 |
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Details of virus | Empty: NO / Enveloped: NO / Host category: ARCHAEA / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Sulfolobus islandicus |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV). |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Sep 19, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 437 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software | Name: SPIDER / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: multiply images by CTF, divide reconstruction by sum of CTF**2 | ||||||||||||
Helical symmerty | Angular rotation/subunit: 24.5 ° / Axial rise/subunit: 2.9 Å / Axial symmetry: C1 | ||||||||||||
3D reconstruction | Method: IHRSR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Nominal pixel size: 1.05 Å / Actual pixel size: 1.05 Å / Details: (Helical Details: IHRSR) / Symmetry type: HELICAL | ||||||||||||
Refinement step | Cycle: LAST
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