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- EMDB-2133: The Structure of Lactococcal Phage TP901-1 by electron microscopy... -

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Basic information

Entry
Database: EMDB / ID: EMD-2133
TitleThe Structure of Lactococcal Phage TP901-1 by electron microscopy: the capsid
Map dataIcosahedral reconstruction of the capsid of the phage TP901-1
Sample
  • Sample: Icosahedral capsid of the lactococcal phage TP901-1
  • Virus: Lactococcus phage TP901-1 (virus)
KeywordsEM / capsid / icosahedral / tp901 / lactococcal phage
Biological speciesLactococcus phage TP901-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsBebeacua C / Lai L / Skovgaard Vegge C / Brondsted L / van Heel M / Veesler D / Cambillau C
CitationJournal: J Virol / Year: 2013
Title: Visualizing a complete Siphoviridae member by single-particle electron microscopy: the structure of lactococcal phage TP901-1.
Authors: Cecilia Bebeacua / Livia Lai / Christina Skovgaard Vegge / Lone Brøndsted / Marin van Heel / David Veesler / Christian Cambillau /
Abstract: Tailed phages are genome delivery machines exhibiting unequaled efficiency acquired over more than 3 billion years of evolution. Siphophages from the P335 and 936 families infect the Gram-positive ...Tailed phages are genome delivery machines exhibiting unequaled efficiency acquired over more than 3 billion years of evolution. Siphophages from the P335 and 936 families infect the Gram-positive bacterium Lactococcus lactis using receptor-binding proteins anchored to the host adsorption apparatus (baseplate). Crystallographic and electron microscopy (EM) studies have shed light on the distinct adsorption strategies used by phages of these two families, suggesting that they might also rely on different infection mechanisms. Here, we report electron microscopy reconstructions of the whole phage TP901-1 (P335 species) and propose a composite EM model of this gigantic molecular machine. Our results suggest conservation of structural proteins among tailed phages and add to the growing body of evidence pointing to a common evolutionary origin for these virions. Finally, we propose that host adsorption apparatus architectures have evolved in correlation with the nature of the receptors used during infection.
History
DepositionJun 11, 2012-
Header (metadata) releaseNov 21, 2012-
Map releaseNov 21, 2012-
UpdateJan 9, 2013-
Current statusJan 9, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2133.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of the capsid of the phage TP901-1
Voxel sizeX=Y=Z: 3.2 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-2.31868172 - 8.4837513
Average (Standard dev.)0.10018362 (±0.67388016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 819.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.23.23.2
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z819.200819.200819.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-2.3198.4840.100

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Supplemental data

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Sample components

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Entire : Icosahedral capsid of the lactococcal phage TP901-1

EntireName: Icosahedral capsid of the lactococcal phage TP901-1
Components
  • Sample: Icosahedral capsid of the lactococcal phage TP901-1
  • Virus: Lactococcus phage TP901-1 (virus)

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Supramolecule #1000: Icosahedral capsid of the lactococcal phage TP901-1

SupramoleculeName: Icosahedral capsid of the lactococcal phage TP901-1 / type: sample / ID: 1000
Details: The sample corresponded to the full phage but only the capsid particles were selected.
Oligomeric state: Icosahedral / Number unique components: 1
Molecular weightExperimental: 13 MDa / Theoretical: 13 MDa

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Supramolecule #1: Lactococcus phage TP901-1

SupramoleculeName: Lactococcus phage TP901-1 / type: virus / ID: 1
Details: The sample contained the full phages with tail and baseplate. Only the capsids were selected.
NCBI-ID: 35345 / Sci species name: Lactococcus phage TP901-1 / Virus type: VIRION / Virus isolate: STRAIN / 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 (100 mM sodium chloride, 10 mM magnesium sulfate, 50 mM Tris [pH 7.5], and 0.01% [wt/vol] gelatin)
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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 80 K / Max: 105 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 130,000 times magnification.
DateJun 1, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Number real images: 200 / Average electron dose: 10 e/Å2

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Image processing

CTF correctionDetails: Images
Final angle assignmentDetails: ICOSAHEDRAL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 1500
DetailsThe particles were submitted to single-particle analysis with icosahedral symmetry using IMAGIC-V

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Atomic model buiding 1

Initial modelPDB ID:
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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