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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5844 | |||||||||
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Title | Subtomogram average of a virus-associated pyramid | |||||||||
![]() | Reconstruction of a virus associated pyramid | |||||||||
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![]() | VAP / archaeovirus / archaea / SIRV2 / Sulfolobus islandicus / viral egress | |||||||||
Function / homology | : / membrane => GO:0016020 / Uncharacterized protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
![]() | Daum B / Kuehlbrandt W | |||||||||
![]() | ![]() Title: Self-assembly of the general membrane-remodeling protein PVAP into sevenfold virus-associated pyramids. Authors: Bertram Daum / Tessa E F Quax / Martin Sachse / Deryck J Mills / Julia Reimann / Özkan Yildiz / Sabine Häder / Cosmin Saveanu / Patrick Forterre / Sonja-Verena Albers / Werner Kühlbrandt ...Authors: Bertram Daum / Tessa E F Quax / Martin Sachse / Deryck J Mills / Julia Reimann / Özkan Yildiz / Sabine Häder / Cosmin Saveanu / Patrick Forterre / Sonja-Verena Albers / Werner Kühlbrandt / David Prangishvili / ![]() Abstract: Viruses have developed a wide range of strategies to escape from the host cells in which they replicate. For egress some archaeal viruses use a pyramidal structure with sevenfold rotational symmetry. ...Viruses have developed a wide range of strategies to escape from the host cells in which they replicate. For egress some archaeal viruses use a pyramidal structure with sevenfold rotational symmetry. Virus-associated pyramids (VAPs) assemble in the host cell membrane from the virus-encoded protein PVAP and open at the end of the infection cycle. We characterize this unusual supramolecular assembly using a combination of genetic, biochemical, and electron microscopic techniques. By whole-cell electron cryotomography, we monitored morphological changes in virus-infected host cells. Subtomogram averaging reveals the VAP structure. By heterologous expression of PVAP in cells from all three domains of life, we demonstrate that the protein integrates indiscriminately into virtually any biological membrane, where it forms sevenfold pyramids. We identify the protein domains essential for VAP formation in PVAP truncation mutants by their ability to remodel the cell membrane. Self-assembly of PVAP into pyramids requires at least two different, in-plane and out-of-plane, protein interactions. Our findings allow us to propose a model describing how PVAP arranges to form sevenfold pyramids and suggest how this small, robust protein may be used as a general membrane-remodeling system. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.3 KB 10.3 KB | Display Display | ![]() |
Images | ![]() ![]() | 124.9 KB 2.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.4 KB | Display | ![]() |
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Full document | ![]() | 77.5 KB | Display | |
Data in XML | ![]() | 499 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of a virus associated pyramid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.663 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Reconstruction of a virus-associated pyramid induced by overexpre...
Entire | Name: Reconstruction of a virus-associated pyramid induced by overexpressing the viral protein PVAP in E. coli |
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Components |
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-Supramolecule #1000: Reconstruction of a virus-associated pyramid induced by overexpre...
Supramolecule | Name: Reconstruction of a virus-associated pyramid induced by overexpressing the viral protein PVAP in E. coli type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: protein forming virus-associated pyramids
Macromolecule | Name: protein forming virus-associated pyramids / type: protein_or_peptide / ID: 1 / Name.synonym: P98, PVAP Details: The gene encoding PVAP was heterologously overexpressed in E. coli to incorporate pyramid-shaped multimers of PVAP into the plasma membrane. Oligomeric state: Multimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 10 KDa / Theoretical: 10 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Uncharacterized protein / GO: GO: 0951408 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 / Details: 50 mM Tris, 300 mM NaCl |
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Grid | Details: Quantifoil 300 mesh R2/2, glow-discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 10 % / Instrument: HOMEMADE PLUNGER Method: Blot for 3-5 seconds from the side where the sample was applied. |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 89 K / Max: 96 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 40,000 times magnification |
Specialist optics | Energy filter - Name: Gatan Tridium GIF |
Date | Mar 12, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Bits/pixel: 32 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 16870 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 10.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 27500 |
Sample stage | Specimen holder: liquid nitrogen cooled / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -60.73 ° / Tilt series - Axis1 - Max angle: 59.20 ° |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Software - Name: PEET, IMOD / Number subtomograms used: 57 |
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