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Yorodumi- EMDB-4457: Dodecameric reconstruction of portal and tail of empty particle o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4457 | ||||||||||||
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Title | Dodecameric reconstruction of portal and tail of empty particle of bacteriophage P68 (subset without tailknob) | ||||||||||||
Map data | Dodecameric reconstruction of portal and tail of empty particle of bacteriophage P68 | ||||||||||||
Sample |
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Biological species | Staphylococcus phage P68 (virus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 Å | ||||||||||||
Authors | Hrebik D / Skubnik K / Fuzik T / Plevka P | ||||||||||||
Funding support | Czech Republic, 3 items
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Citation | Journal: Sci Adv / Year: 2019 Title: Structure and genome ejection mechanism of phage P68. Authors: Dominik Hrebík / Dana Štveráková / Karel Škubník / Tibor Füzik / Roman Pantůček / Pavel Plevka / Abstract: Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect ...Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm. | ||||||||||||
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_4457.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-4457-v30.xml emd-4457.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4457_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_4457.png | 100.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4457 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4457 | HTTPS FTP |
-Validation report
Summary document | emd_4457_validation.pdf.gz | 235 KB | Display | EMDB validaton report |
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Full document | emd_4457_full_validation.pdf.gz | 234.1 KB | Display | |
Data in XML | emd_4457_validation.xml.gz | 11.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4457 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4457 | HTTPS FTP |
-Related structure data
Related structure data | 4435C 4436C 4437C 4438C 4440C 4442C 4449C 4450C 4451C 4453C 4454C 4455C 4456C 4458C 4459C 6iabC 6iacC 6iatC 6iawC 6ib1C 6q3gC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4457.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Dodecameric reconstruction of portal and tail of empty particle of bacteriophage P68 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.126 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 : Staphylococcus phage P68
Entire | Name: Staphylococcus phage P68 (virus) |
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Components |
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-Supramolecule #1: Staphylococcus phage P68
Supramolecule | Name: Staphylococcus phage P68 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 204090 / Sci species name: Staphylococcus phage P68 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Staphylococcus aureus (bacteria) / Strain: dTarM 4220 |
Molecular weight | Theoretical: 19.7 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 485.0 Å / T number (triangulation number): 4 |
-Supramolecule #2: Portal protein complex in native virion
Supramolecule | Name: Portal protein complex in native virion / type: complex / ID: 2 / Parent: 1 Details: portal protein in complex with inner core protein located in the special icosahedral five-fold symmetry vertex |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
-Supramolecule #3: Lower collar protein
Supramolecule | Name: Lower collar protein / type: complex / ID: 3 / Parent: 1 Details: lower collar protein is located below the portal protein |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
-Supramolecule #4: Tail fiber protein
Supramolecule | Name: Tail fiber protein / type: complex / ID: 4 / Parent: 1 / Details: Trimer of tail fiber protein |
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-Supramolecule #5: Portal protein
Supramolecule | Name: Portal protein / type: complex / ID: 5 / Parent: 1 Details: portal protein gp19 located in the special icosahedral five-fold symmetry vertex |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
-Supramolecule #6: Inner core protein
Supramolecule | Name: Inner core protein / type: complex / ID: 6 / Parent: 1 Details: helix of inner core protein located above the wing domain of portal protein |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: NITROGEN | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 2s; blot force -2; 3.6 ul of sample. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-7 / Number grids imaged: 2 / Number real images: 2891 / Average exposure time: 1.0 sec. / Average electron dose: 21.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |