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- EMDB-4454: Dodecameric reconstruction of portal and tail of genome release i... -

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Basic information

Entry
Database: EMDB / ID: EMD-4454
TitleDodecameric reconstruction of portal and tail of genome release intermediate state of bacteriophage P68
Map dataDodecameric reconstruction of portal and tail of genome release intermediate state of bacteriophage P68
Sample
  • Virus: Staphylococcus phage P68 (virus)
    • Complex: Portal protein complex in native virion
    • Complex: Lower collar protein
    • Complex: Portal protein
    • Complex: Inner core protein
    • Complex: Tail fiber protein
Biological speciesStaphylococcus phage P68 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.8 Å
AuthorsHrebik D / Skubnik K / Fuzik T / Plevka P
Funding support Czech Republic, 3 items
OrganizationGrant numberCountry
Czech Science Foundation15-21631Y Czech Republic
European Molecular Biology Organization3041 Czech Republic
Czech Science Foundation18-17810S Czech Republic
CitationJournal: 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
DepositionDec 2, 2018-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4454.png

Downloads & links

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Map

FileDownload / File: emd_4454.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDodecameric reconstruction of portal and tail of genome release intermediate state of bacteriophage P68
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 440 pix.
= 935.44 Å		2.13 Å/pix.
x 440 pix.
= 935.44 Å		2.13 Å/pix.
x 440 pix.
= 935.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.126 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.0520508 - 0.12735856
Average (Standard dev.)0.00025510867 (±0.005427294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-220-220-220
Dimensions440440440
Spacing440440440
CellA=B=C: 935.43994 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1262.1262.126
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z935.440935.440935.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-220-220-220
NC/NR/NS440440440
D min/max/mean-0.0520.1270.000

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Supplemental data

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Sample components

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Entire : Staphylococcus phage P68

EntireName: Staphylococcus phage P68 (virus)
Components
  • Virus: Staphylococcus phage P68 (virus)
    • Complex: Portal protein complex in native virion
    • Complex: Lower collar protein
    • Complex: Portal protein
    • Complex: Inner core protein
    • Complex: Tail fiber protein

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Supramolecule #1: Staphylococcus phage P68

SupramoleculeName: Staphylococcus phage P68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 204090 / Sci species name: Staphylococcus phage P68 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Staphylococcus aureus (bacteria) / Strain: dTarM 4220
Virus shellShell ID: 1 / Name: Capsid / Diameter: 485.0 Å / T number (triangulation number): 4

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Supramolecule #2: Portal protein complex in native virion

SupramoleculeName: Portal protein complex in native virion / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4
Details: portal protein in complex with inner core protein located in the special icosahedral five-fold symmetry vertex
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Supramolecule #3: Lower collar protein

SupramoleculeName: Lower collar protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: lower collar protein is located below the portal protein
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Supramolecule #4: Portal protein

SupramoleculeName: Portal protein / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1
Details: portal protein gp19 located in the special icosahedral five-fold symmetry vertex
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Supramolecule #5: Inner core protein

SupramoleculeName: Inner core protein / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4 / Details: helix of inner core protein located above the wing
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Supramolecule #6: Tail fiber protein

SupramoleculeName: Tail fiber protein / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #3 / Details: Trimer of tail fiber protein
Source (natural)Organism: Staphylococcus phage P68 (virus)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTristris(hydroxymethyl)aminomethane
10.0 mMCaClcalcium chloride
10.0 mMNaClsodium chloride
VitrificationCryogen 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.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4040
CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Startup modelType of model: INSILICO MODEL
In silico model: the icosahedral initial model was created by a random "de novo" initial model method as described in - Guo F., Jiang W., Methods in molecular biology, 2014.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 18.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 1506
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 2020 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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