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- EMDB-1715: Asymmetric structure of the infectious Prochlorococcus Cyanophage... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1715 | |||||||||
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Title | Asymmetric structure of the infectious Prochlorococcus Cyanophage P-SSP7 | |||||||||
![]() | Asymmetric structure of the infectious Prochlorococcus Cyanophage P-SSP7 | |||||||||
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![]() | Marine Podovirus / T7-like virus / infects Prochlorococcus MED4 | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 9.2 Å | |||||||||
![]() | Liu X / Zhang Q / Murata K / Baker ML / Sullivan MB / Fu C / Dougherty M / Schmid MF / Osburne MS / Chisholm SW / Chiu W | |||||||||
![]() | ![]() Title: Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Authors: Xiangan Liu / Qinfen Zhang / Kazuyoshi Murata / Matthew L Baker / Matthew B Sullivan / Caroline Fu / Matthew T Dougherty / Michael F Schmid / Marcia S Osburne / Sallie W Chisholm / Wah Chiu / ![]() Abstract: Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single-particle cryo-electron microscopy yields icosahedral and asymmetrical structures of ...Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single-particle cryo-electron microscopy yields icosahedral and asymmetrical structures of infectious P-SSP7 with 4.6-A and 9-A resolution, respectively. The asymmetric reconstruction reveals how symmetry mismatches are accommodated among five of the gene products at the portal vertex. Reconstructions of infectious and empty particles show a conformational change of the 'valve' density in the nozzle, an orientation difference in the tail fibers, a disordering of the C terminus of the portal protein and the disappearance of the core proteins. In addition, cryo-electron tomography of P-SSP7 infecting Prochlorococcus showed the same tail-fiber conformation as that in empty particles. Our observations suggest a mechanism whereby, upon binding to the host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers DNA release. | |||||||||
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 | ![]() | 53 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.3 KB 11.3 KB | Display Display | ![]() |
Images | ![]() | 261.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Asymmetric structure of the infectious Prochlorococcus Cyanophage P-SSP7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.34 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 : Cyanophage P-SSP7
Entire | Name: Cyanophage P-SSP7 |
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Components |
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-Supramolecule #1000: Cyanophage P-SSP7
Supramolecule | Name: Cyanophage P-SSP7 / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Prochlorococcus phage P-SSP7
Supramolecule | Name: Prochlorococcus phage P-SSP7 / type: virus / ID: 1 / Name.synonym: Virus Details: gp8, gp10, gp11, gp12, gp14, gp15, gp16, gp 17, dsDNA (portal, capsid, adaptor, nozzle, core proteins, tail fibers, DNA) NCBI-ID: 268748 / Sci species name: Prochlorococcus phage P-SSP7 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Virus |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Diameter: 655 Å / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 / Details: 100 mM Tris-HCl, 100 mM MgSO4, and 30 mM NaCl |
Staining | Type: NEGATIVE / Details: No stain |
Grid | Details: 200 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 30 % / Chamber temperature: 101 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 2 seconds 2 times before plunging. |
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Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Min: 4.5 K / Max: 102 K / Average: 101 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification |
Specialist optics | Energy filter - Name: JEOL / Energy filter - Lower energy threshold: 15.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Details | MDS |
Date | Aug 31, 2007 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 1059 / Average electron dose: 20 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: Side entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER |
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Image processing
Details | The particles were selected from the 36,000 raw particles used for icosahedral reconstruction, which have consistent orientations in the last few iterations of the asymmetric reconstruction of P-SSP7. |
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CTF correction | Details: Each micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MPSA Details: The map was directly reconstructed from raw particle images without imposing any symmetry. Number images used: 15000 |
Final angle assignment | Details: EMAN: Z axis along 5-fold and Y axis along 2-fold asymmetry axis. |