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Yorodumi- EMDB-3131: Visualizing the Adsorption of Cyanophage P-SSP7 to the Marine Cya... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3131 | |||||||||
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Title | Visualizing the Adsorption of Cyanophage P-SSP7 to the Marine Cyanobacterium Prochlorococcus MED4 by Electron Cryo-Tomography | |||||||||
Map data | pre-infection conformation of P-SSP7 bacteriophage | |||||||||
Sample |
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Keywords | cryo-electron tomography / bacteriophage / cyanobacteria | |||||||||
Biological species | Prochlorococcus phage P-SSP7 (virus) | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
Authors | Murata K / Zhang Q / Fu C / Liu X / Sullivan M / Coleman M / Osburne M / Schmid MF / Chisholm S / Chiu W | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus. Authors: Kazuyoshi Murata / Qinfen Zhang / Jesús Gerardo Galaz-Montoya / Caroline Fu / Maureen L Coleman / Marcia S Osburne / Michael F Schmid / Matthew B Sullivan / Sallie W Chisholm / Wah Chiu / Abstract: Marine cyanobacteria perform roughly a quarter of global carbon fixation, and cyanophages that infect them liberate some of this carbon during infection and cell lysis. Studies of the cyanobacterium ...Marine cyanobacteria perform roughly a quarter of global carbon fixation, and cyanophages that infect them liberate some of this carbon during infection and cell lysis. Studies of the cyanobacterium Prochlorococcus MED4 and its associated cyanophage P-SSP7 have revealed complex gene expression dynamics once infection has begun, but the initial cyanophage-host interactions remain poorly understood. Here, we used single particle cryo-electron tomography (cryo-ET) to investigate cyanophage-host interactions in this model system, based on 170 cyanophage-to-host adsorption events. Subtomogram classification and averaging revealed three main conformations characterized by different angles between the phage tail and the cell surface. Namely, phage tails were (i) parallel to, (ii) ~45 degrees to, or (iii) perpendicular to the cell surface. Furthermore, different conformations of phage tail fibers correlated with the aforementioned orientations of the tails. We also observed density beyond the tail tip in vertically-oriented phages that had penetrated the cell wall, capturing the final stage of adsorption. Together, our data provide a quantitative characterization of the orientation of phages as they adsorb onto cells, and suggest that cyanophages that abut their cellular targets are only transiently in the "perpendicular" orientation required for successful infection. | |||||||||
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_3131.map.gz | 9.4 MB | EMDB map data format | |
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Header (meta data) | emd-3131-v30.xml emd-3131.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | EMD-3131.jpg | 178.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3131 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3131 | HTTPS FTP |
-Validation report
Summary document | emd_3131_validation.pdf.gz | 221.9 KB | Display | EMDB validaton report |
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Full document | emd_3131_full_validation.pdf.gz | 221.1 KB | Display | |
Data in XML | emd_3131_validation.xml.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3131 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3131 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3131.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | pre-infection conformation of P-SSP7 bacteriophage | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 9.36 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 : Pre-infection comformation of Prochlorococcus phage P-SSP7
Entire | Name: Pre-infection comformation of Prochlorococcus phage P-SSP7 |
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Components |
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-Supramolecule #1000: Pre-infection comformation of Prochlorococcus phage P-SSP7
Supramolecule | Name: Pre-infection comformation of Prochlorococcus phage 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 / NCBI-ID: 268748 / Sci species name: Prochlorococcus phage P-SSP7 / Sci species strain: P-SSP7 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Prochlorococcus (bacteria) / Strain: MED4 / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / Diameter: 655 Å / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 Details: 100 mM Tris-HCl (pH 7.5), 100 mM MgSO4, and 30 mM NaCl |
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Grid | Details: R3.5/1 Quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 120 K / Instrument: LEICA EM CPC Method: Grids with sample solution were quickly frozen in liquid ethane. |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Average: 90 K |
Specialist optics | Energy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 30.0 eV |
Date | May 16, 2008 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 80 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: 4.1 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 20000 |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 62 ° |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution method: OTHER / Software - Name: EMAN1 / Number subtomograms used: 44 |
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