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- EMDB-8203: Neck and connector complexes of native phi812-K420 bacteriophage,... -

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Basic information

Entry
Database: EMDB / ID: EMD-8203
TitleNeck and connector complexes of native phi812-K420 bacteriophage, C6 symmetry reconstruction
Map dataNone
Sample
  • Virus: Staphylococcus phage 812 (virus)
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 28.3 Å
AuthorsNovacek J / Siborova M / Benesik M / Pantucek R / Doskar J / Plevka P
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure and genome release of Twort-like Myoviridae phage with a double-layered baseplate.
Authors: Jiří Nováček / Marta Šiborová / Martin Benešík / Roman Pantůček / Jiří Doškař / Pavel Plevka /
Abstract: Bacteriophages from the family Myoviridae use double-layered contractile tails to infect bacteria. Contraction of the tail sheath enables the tail tube to penetrate through the bacterial cell wall ...Bacteriophages from the family Myoviridae use double-layered contractile tails to infect bacteria. Contraction of the tail sheath enables the tail tube to penetrate through the bacterial cell wall and serve as a channel for the transport of the phage genome into the cytoplasm. However, the mechanisms controlling the tail contraction and genome release of phages with "double-layered" baseplates were unknown. We used cryo-electron microscopy to show that the binding of the Twort-like phage phi812 to the Staphylococcus aureus cell wall requires a 210° rotation of the heterohexameric receptor-binding and tripod protein complexes within its baseplate about an axis perpendicular to the sixfold axis of the tail. This rotation reorients the receptor-binding proteins to point away from the phage head, and also results in disruption of the interaction of the tripod proteins with the tail sheath, hence triggering its contraction. However, the tail sheath contraction of Myoviridae phages is not sufficient to induce genome ejection. We show that the end of the phi812 double-stranded DNA genome is bound to one protein subunit from a connector complex that also forms an interface between the phage head and tail. The tail sheath contraction induces conformational changes of the neck and connector that result in disruption of the DNA binding. The genome penetrates into the neck, but is stopped at a bottleneck before the tail tube. A subsequent structural change of the tail tube induced by its interaction with the S. aureus cell is required for the genome's release.
History
DepositionMay 23, 2016-
Header (metadata) releaseAug 10, 2016-
Map releaseAug 10, 2016-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8203.png

Downloads & links

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Map

FileDownload / File: emd_8203.map.gz / Format: CCP4 / Size: 7.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.44 Å/pix.
x 200 pix.
= 688. Å		3.44 Å/pix.
x 100 pix.
= 344. Å		3.44 Å/pix.
x 100 pix.
= 344. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 3.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-4.304957 - 5.252329
Average (Standard dev.)0.11061307 (±0.75126654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-260
Dimensions100100200
Spacing100100200
CellA: 344.0 Å / B: 344.0 Å / C: 688.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.443.443.44
M x/y/z100100200
origin x/y/z0.0000.0000.000
length x/y/z344.000344.000688.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-260
NC/NR/NS100100200
D min/max/mean-4.3055.2520.111

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Supplemental data

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Sample components

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Entire : Staphylococcus phage 812

EntireName: Staphylococcus phage 812 (virus)
Components
  • Virus: Staphylococcus phage 812 (virus)

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Supramolecule #1: Staphylococcus phage 812

SupramoleculeName: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 307898 / Sci species name: Staphylococcus phage 812 / Sci species strain: K420 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Staphylococcus aureus (bacteria)
Virus shellShell ID: 1 / Diameter: 1100.0 Å / T number (triangulation number): 16

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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

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTrisHCltris
10.0 mMNaClsodium chloride
10.0 mMCaCl2calcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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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 / Average exposure time: 0.86 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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

Details1
CTF correctionSoftware - Name: EMAN (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 28.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: J3DR / Number images used: 1494
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: JALIGN
Final angle assignmentType: PROJECTION MATCHING / Software - Name: JALIGN

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