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- EMDB-2647: electron cryo-microscopy of 1358 Lactococcus phage mature empty capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-2647
Titleelectron cryo-microscopy of 1358 Lactococcus phage mature empty capsid
Map datalactococcus phage 1358 mature empty capsid
Sample
  • Sample: lactococcus phage 1358 mature empty capsid
  • Virus: Lactococcus phage 1358 (virus)
Keywordsphage / capsid / cryo-EM
Biological speciesLactococcus phage 1358 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsSpinelli S / Bebeacua C / Orlov I / Tremblay D / Klaholz B / Moineau S / Cambillau C
CitationJournal: J Virol / Year: 2014
Title: Cryo-electron microscopy structure of lactococcal siphophage 1358 virion.
Authors: Silvia Spinelli / Cecilia Bebeacua / Igor Orlov / Denise Tremblay / Bruno P Klaholz / Sylvain Moineau / Christian Cambillau /
Abstract: Lactococcus lactis, a Gram(+) lactic acid-producing bacterium used for the manufacture of several fermented dairy products, is subject to infection by diverse virulent tailed phages, leading to ...Lactococcus lactis, a Gram(+) lactic acid-producing bacterium used for the manufacture of several fermented dairy products, is subject to infection by diverse virulent tailed phages, leading to industrial fermentation failures. This constant viral risk has led to a sustained interest in the study of their biology, diversity, and evolution. Lactococcal phages now constitute a wide ensemble of at least 10 distinct genotypes within the Caudovirales order, many of them belonging to the Siphoviridae family. Lactococcal siphophage 1358, currently the only member of its group, displays a noticeably high genomic similarity to some Listeria phages as well as a host range limited to a few L. lactis strains. These genomic and functional characteristics stimulated our interest in this phage. Here, we report the cryo-electron microscopy structure of the complete 1358 virion. Phage 1358 exhibits noteworthy features, such as a capsid with dextro handedness and protruding decorations on its capsid and tail. Observations of the baseplate of virion particles revealed at least two conformations, a closed and an open, activated form. Functional assays uncovered that the adsorption of phage 1358 to its host is Ca(2+) independent, but this cation is necessary to complete its lytic cycle. Taken together, our results provide the complete structural picture of a unique lactococcal phage and expand our knowledge on the complex baseplate of phages of the Siphoviridae family.
IMPORTANCE: Phages of Lactococcus lactis are investigated mainly because they are sources of milk fermentation failures in the dairy industry. Despite the availability of several antiphage measures, ...IMPORTANCE: Phages of Lactococcus lactis are investigated mainly because they are sources of milk fermentation failures in the dairy industry. Despite the availability of several antiphage measures, new phages keep emerging in this ecosystem. In this study, we provide the cryo-electron microscopy reconstruction of a unique lactococcal phage that possesses genomic similarity to particular Listeria phages and has a host range restricted to only a minority of L. lactis strains. The capsid of phage 1358 displays the almost unique characteristic of being dextro handed. Its capsid and tail exhibit decorations that we assigned to nonspecific sugar binding modules. We observed the baseplate of 1358 in two conformations, a closed and an open form. We also found that the adsorption to its host, but not infection, is Ca(2+) independent. Overall, this study advances our understanding of the adhesion mechanisms of siphophages.
History
DepositionMay 14, 2014-
Header (metadata) releaseMay 28, 2014-
Map releaseMay 28, 2014-
UpdateNov 19, 2014-
Current statusNov 19, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2647-Emp...

Downloads & links

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Map

FileDownload / File: emd_2647.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlactococcus phage 1358 mature empty capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.84 Å/pix.
x 256 pix.
= 983.04 Å		3.84 Å/pix.
x 256 pix.
= 983.04 Å		3.84 Å/pix.
x 256 pix.
= 983.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.25 / Movie #1: 5.25
Minimum - Maximum-15.97627735 - 19.651067730000001
Average (Standard dev.)0.0 (±1.6559155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 983.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.843.843.84
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z983.040983.040983.040
α/β/γ90.00090.00090.000
start NX/NY/NZ0-51-100
NX/NY/NZ82103201
MAP C/R/S123
start NC/NR/NS-128-127-128
NC/NR/NS256256256
D min/max/mean-15.97619.6510.000

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Supplemental data

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Sample components

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Entire : lactococcus phage 1358 mature empty capsid

EntireName: lactococcus phage 1358 mature empty capsid
Components
  • Sample: lactococcus phage 1358 mature empty capsid
  • Virus: Lactococcus phage 1358 (virus)

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Supramolecule #1000: lactococcus phage 1358 mature empty capsid

SupramoleculeName: lactococcus phage 1358 mature empty capsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Lactococcus phage 1358

SupramoleculeName: Lactococcus phage 1358 / type: virus / ID: 1 / NCBI-ID: 741942 / Sci species name: Lactococcus phage 1358 / Sci species strain: SMQ-388 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Lactococcus lactis (lactic acid bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 635 Å / T number (triangulation number): 6

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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

BufferDetails: 50 mM Tris-HCl pH 7.5, 100 mM NaCl, 8 mM MgSO4
GridDetails: 200 mesh, quantifoil 1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: blot 2 seconds, force 4

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Electron microscopy

MicroscopeFEI POLARA 300
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
DateNov 11, 2011
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 1.92 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0015 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsIMAGIC software package, angular reconstitution - Euler angles determination and refinement
CTF correctionDetails: each microphotograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: Imagic-V / Number images used: 1951

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