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- EMDB-4450: Localized reconstruction of tail-spike of bacteriophage P68 -

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Basic information

Entry
Database: EMDB / ID: EMD-4450
TitleLocalized reconstruction of tail-spike of bacteriophage P68
Map dataLocalized reconstruction of tail-spike of bacteriophage P68
Sample
  • Virus: Staphylococcus phage P68 (virus)
    • Protein or peptide: Tail-spike of bacteriophage P68
Biological speciesStaphylococcus phage P68 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 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 1, 2018-
Header (metadata) releaseNov 6, 2019-
Map releaseNov 6, 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: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4450.png

Downloads & links

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Map

FileDownload / File: emd_4450.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocalized reconstruction of tail-spike of bacteriophage P68
Voxel sizeX=Y=Z: 2.126 Å
Density
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.007
Minimum - Maximum-0.08456932 - 0.12854412
Average (Standard dev.)-0.00021772903 (±0.004295795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 212.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1262.1262.126
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z212.600212.600212.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0850.129-0.000

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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)
    • Protein or peptide: Tail-spike of bacteriophage P68

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Supramolecule #1: Staphylococcus phage P68

SupramoleculeName: Staphylococcus phage P68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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
Molecular weightTheoretical: 6.9 KDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 480.0 Å / T number (triangulation number): 4

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Macromolecule #1: Tail-spike of bacteriophage P68

MacromoleculeName: Tail-spike of bacteriophage P68 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: lysozyme
SequenceString: MNDQEKIDKF THSYINDDFG LTIDQLVPKV KGYGRFNVWL GGNESKIRQV LKAVKEIGVS PTLFAVYEKN EGFSSGLGW LNHTSARGDY LTDAKFIARK LVSQSKQAGQ PSWYDAGNIV HFVPQDVQRK GNADFAKNMK A GTIGRAYI PLTAAATWAA YYPLGLKASY ...String:
MNDQEKIDKF THSYINDDFG LTIDQLVPKV KGYGRFNVWL GGNESKIRQV LKAVKEIGVS PTLFAVYEKN EGFSSGLGW LNHTSARGDY LTDAKFIARK LVSQSKQAGQ PSWYDAGNIV HFVPQDVQRK GNADFAKNMK A GTIGRAYI PLTAAATWAA YYPLGLKASY NKVQNYGNPF LDGANTILAW GGKLDGKGGS PSDSSDSGSS GD SGSSLLA LAKQAMQELL KKIQDALQWD VHSIGSDKFF SNDYFTLEKT FNNTYHIKMT IGLLDSLKKL IDS VQVDSG SSSSNPTDDD GDHKPISGKS VKPNGKSGRV IGGNWTYAQL PEKYKKAIGV PLFKKEYLYK PGNI FPQTG NAGQCTELTW AYMSQLHGKR QPTDDGQITN GQRVWYVYKK LGAKTTHNPT VGYGFSSKPP YLQAT AYGI GHTGVVVAVF EDGSFLVANY NVPPYVAPSR VVLYTLINGV PNNAGDNIVF FSGIA

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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 chloridesodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: NITROGEN
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 37218 / Details: Manual selection in EMAN
CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Startup modelType of model: INSILICO MODEL
In silico model: An initial model was calculated by applying Euler angles from C5 reconstruction of the bacteriophage capsid
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Details: Only side views (particles oriented perpendicularly to the electron beam) were selected from the 2D classification.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 6121
FSC plot (resolution estimation)

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