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- EMDB-4054: bacteriophage phi812K1-420 major capsid protein -

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Basic information

Entry
Database: EMDB / ID: EMD-4054
Titlebacteriophage phi812K1-420 major capsid protein
Map databacteriophage phi812K1-420 cement protein
Sample
  • Virus: Staphylococcus phage 812 (virus)
    • Protein or peptide: polyalanine chain built in bacteriophage phi812K1-420 cement protein density map
Biological speciesStaphylococcus phage 812 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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
DepositionJul 14, 2016-
Header (metadata) releaseJul 26, 2017-
Map releaseJul 26, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5lij
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4054.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbacteriophage phi812K1-420 cement protein
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 3 / Movie #1: 3
Minimum - Maximum-6.1688185 - 10.184282
Average (Standard dev.)0.00000000229 (±0.625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 88.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z88.32088.32088.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-6.16910.1840.000

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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)
    • Protein or peptide: polyalanine chain built in bacteriophage phi812K1-420 cement protein density map

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Supramolecule #1: Staphylococcus phage 812

SupramoleculeName: Staphylococcus phage 812 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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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Macromolecule #1: polyalanine chain built in bacteriophage phi812K1-420 cement prot...

MacromoleculeName: polyalanine chain built in bacteriophage phi812K1-420 cement protein density map
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812 (virus)
Molecular weightTheoretical: 10.821817 KDa
Recombinant expressionOrganism: Staphylococcaceae (Staphylococcus group)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAA

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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 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTrisHCltris
10.0 mMNaClSodium chloridesodium chloride
10.0 mMCaCl2calcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
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 / Average exposure time: 0.86 sec. / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: NOT APPLICABLE / Software - Name: JALIGN
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: NOT APPLICABLE / Software - Name: JALIGN
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: J3DR / Number images used: 12018

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