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- PDB-6d5f: Cryo-EM reconstruction of membrane-enveloped filamentous virus SF... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d5f | ||||||
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Title | Cryo-EM reconstruction of membrane-enveloped filamentous virus SFV1 (Sulfolobus filamentous virus 1) | ||||||
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![]() | VIRUS / filamentous virus / helical symmetry / membrane enveloped virus | ||||||
Function / homology | DNA / DNA (> 10) / DNA (> 100)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
![]() | Wang, F. / Osinski, T. / Liu, Y. / Krupovic, M. / Prangishvili, D. / Egelman, E.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile. Authors: Ying Liu / Tomasz Osinski / Fengbin Wang / Mart Krupovic / Stefan Schouten / Peter Kasson / David Prangishvili / Edward H Egelman / ![]() ![]() ![]() Abstract: Different forms of viruses that infect archaea inhabiting extreme environments continue to be discovered at a surprising rate, suggesting that the current sampling of these viruses is sparse. We ...Different forms of viruses that infect archaea inhabiting extreme environments continue to be discovered at a surprising rate, suggesting that the current sampling of these viruses is sparse. We describe here Sulfolobus filamentous virus 1 (SFV1), a membrane-enveloped virus infecting Sulfolobus shibatae. The virus encodes two major coat proteins which display no apparent sequence similarity with each other or with any other proteins in databases. We have used cryo-electron microscopy at 3.7 Å resolution to show that these two proteins form a nearly symmetrical heterodimer, which wraps around A-form DNA, similar to what has been shown for SIRV2 and AFV1, two other archaeal filamentous viruses. The thin (∼ 20 Å) membrane of SFV1 is mainly archaeol, a lipid species that accounts for only 1% of the host lipids. Our results show how relatively conserved structural features can be maintained across evolution by both proteins and lipids that have diverged considerably. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7797MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 22020.135 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 15792.202 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: DNA chain | Mass: 103678.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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 |
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Sample preparation
Component | Name: Sulfolobus filamentous virus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 6 / Details: 20 mM Tris-acetate, 250 mM sodium chloride, pH 6.0 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 90 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 2 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) Details: Images were stored containing 24 fractions, where each fraction corresponded to a dose of ~2 electrons per Angstrom^2. |
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Processing
Software | Name: PHENIX / Version: dev_2919: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 21.02572 ° / Axial rise/subunit: 2.76412 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87803 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.7 Å |