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- EMDB-2459: Structure and Host Adhesion Mechanism of Virulent Lactococcal Phage p2 -

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Basic information

Entry
Database: EMDB / ID: EMD-2459
TitleStructure and Host Adhesion Mechanism of Virulent Lactococcal Phage p2
Map dataIcosahedral reconstruction of the capsid of p2 phage
Sample
  • Sample: Icosahedral capsid of the lactococcal phage p2
  • Virus: Lactococcus phage p2 (virus)
KeywordsEM / capsid / icosahedral / p2 / lactococcal phage
Biological speciesLactococcus phage p2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsBebeacua C / Tremblay D / Farenc C / Chapot MP / Sadovskaya I / van Heel M / Veesler D / Moineau S / Cambillau C
CitationJournal: J Virol / Year: 2013
Title: Structure, adsorption to host, and infection mechanism of virulent lactococcal phage p2.
Authors: Cecilia Bebeacua / Denise Tremblay / Carine Farenc / Marie-Pierre Chapot-Chartier / Irina Sadovskaya / Marin van Heel / David Veesler / Sylvain Moineau / Christian Cambillau /
Abstract: Lactococcal siphophages from the 936 and P335 groups infect the Gram-positive bacterium Lactococcus lactis using receptor binding proteins (RBPs) attached to their baseplate, a large multiprotein ...Lactococcal siphophages from the 936 and P335 groups infect the Gram-positive bacterium Lactococcus lactis using receptor binding proteins (RBPs) attached to their baseplate, a large multiprotein complex at the distal part of the tail. We have previously reported the crystal and electron microscopy (EM) structures of the baseplates of phages p2 (936 group) and TP901-1 (P335 group) as well as the full EM structure of the TP901-1 virion. Here, we report the complete EM structure of siphophage p2, including its capsid, connector complex, tail, and baseplate. Furthermore, we show that the p2 tail is characterized by the presence of protruding decorations, which are related to adhesins and are likely contributed by the major tail protein C-terminal domains. This feature is reminiscent of the tail of Escherichia coli phage λ and Bacillus subtilis phage SPP1 and might point to a common mechanism for establishing initial interactions with their bacterial hosts. Comparative analyses showed that the architecture of the phage p2 baseplate differs largely from that of lactococcal phage TP901-1. We quantified the interaction of its RBP with the saccharidic receptor and determined that specificity is due to lower k(off) values of the RBP/saccharidic dissociation. Taken together, these results suggest that the infection of L. lactis strains by phage p2 is a multistep process that involves reversible attachment, followed by baseplate activation, specific attachment of the RBPs to the saccharidic receptor, and DNA ejection.
History
DepositionSep 11, 2013-
Header (metadata) releaseMar 19, 2014-
Map releaseMar 19, 2014-
UpdateMar 19, 2014-
Current statusMar 19, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2459.png

Downloads & links

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Map

FileDownload / File: emd_2459.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of the capsid of p2 phage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 200 pix.
= 353. Å		1.77 Å/pix.
x 200 pix.
= 353. Å		1.77 Å/pix.
x 200 pix.
= 353. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.1.7651.7651.765
CCP4 map header1.7651.7651.765
EM Navigator Movie #13.533.533.53
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-5.81779385 - 6.75304365
Average (Standard dev.)0.07196167 (±0.82266712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 353.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7651.7651.765
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z353.000353.000353.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-5.8186.7530.072

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Supplemental data

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Sample components

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Entire : Icosahedral capsid of the lactococcal phage p2

EntireName: Icosahedral capsid of the lactococcal phage p2
Components
  • Sample: Icosahedral capsid of the lactococcal phage p2
  • Virus: Lactococcus phage p2 (virus)

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Supramolecule #1000: Icosahedral capsid of the lactococcal phage p2

SupramoleculeName: Icosahedral capsid of the lactococcal phage p2 / type: sample / ID: 1000
Details: The sample corresponded to the full phage but only the capsid particles were selected.
Oligomeric state: 60-mer / Number unique components: 1
Molecular weightExperimental: 13 MDa / Theoretical: 13 MDa

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Supramolecule #1: Lactococcus phage p2

SupramoleculeName: Lactococcus phage p2 / type: virus / ID: 1
Details: The sample contained the full phages with tail and baseplate. Only the capsids were selected.
NCBI-ID: 254252 / Sci species name: Lactococcus phage p2 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Lactococcus lactis (lactic acid bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 13 MDa / Theoretical: 13 MDa
Virus shellShell ID: 1 / Diameter: 600 Å / T number (triangulation number): 7

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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

BufferpH: 7.5
Details: SM buffer (50 mM Tris-HCl, 100 mM NaCl, 8 mM MgSO4)
GridDetails: Quantifoil grids were glow discharged for 20 seconds
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureMin: 80 K / Max: 105 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 130,000 times magnification.
Specialist opticsEnergy filter - Name: FEI
DateFeb 1, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Number real images: 200 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were submitted to single-particle analysis with icosahedral symmetry using IMAGIC-V
CTF correctionDetails: Images
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 3329
Final angle assignmentDetails: ICOSAHEDRAL

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Atomic model buiding 1

Initial modelPDB ID:

1ohg

SoftwareName: Chimera
DetailsProtocol: Rigid body. Manually fitted 60 copies of the hexamer of HK97. Every hexamer was refined using Chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 10

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