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- EMDB-2340: The electron microscopy reconstruction of the baseplate of lactoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-2340
TitleThe electron microscopy reconstruction of the baseplate of lactococcal phage Tuc2009.
Map dataReconstruction of the baseplate of lactococcal phage Tuc2009
Sample
  • Sample: Baseplate of lactoccocal phage Tuc2009
  • Virus: Lactococcus phage Tuc2009 (virus)
Keywordslactococcal phage / tuc2009 / baseplate / electron microscopy / single-particle
Biological speciesLactococcus phage Tuc2009 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 36.0 Å
AuthorsCollins B / Bebeacua C / Mahony J / Douillard F / Veesler D / Blangy B / Cambillau C / van Sinderen D
CitationJournal: J Virol / Year: 2013
Title: Structure and functional analysis of the host recognition device of lactococcal phage tuc2009.
Authors: Barry Collins / Cecilia Bebeacua / Jennifer Mahony / Stéphanie Blangy / François P Douillard / David Veesler / Christian Cambillau / Douwe van Sinderen /
Abstract: Many phages employ a large heteropolymeric organelle located at the tip of the tail, termed the baseplate, for host recognition. Contrast electron microscopy (EM) of the lactococcal phage Tuc2009 ...Many phages employ a large heteropolymeric organelle located at the tip of the tail, termed the baseplate, for host recognition. Contrast electron microscopy (EM) of the lactococcal phage Tuc2009 baseplate and its host-binding subunits, the so-called tripods, allowed us to obtain a low-resolution structural image of this organelle. Structural comparisons between the baseplate of the related phage TP901-1 and that of Tuc2009 demonstrated that they are highly similar, except for the presence of an additional protein in the Tuc2009 baseplate (BppATuc2009), which is attached to the top of the Tuc2009 tripod structure. Recombinantly produced Tuc2009 or TP901-1 tripods were shown to bind specifically to their particular host cell surfaces and are capable of almost fully and specifically eliminating Tuc2009 or TP901-1 phage adsorption, respectively. In the case of Tuc2009, such adsorption-blocking ability was reduced in tripods that lacked BppATuc2009, indicating that this protein increases the binding specificity and/or affinity of the Tuc2009 tripod to its host receptor.
History
DepositionMar 27, 2013-
Header (metadata) releaseApr 3, 2013-
Map releaseJun 12, 2013-
UpdateJul 17, 2013-
Current statusJul 17, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.001
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.001
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2340.png

Downloads & links

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Map

FileDownload / File: emd_2340.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the baseplate of lactococcal phage Tuc2009
Voxel sizeX=Y=Z: 4.95 Å
Density
Contour LevelBy AUTHOR: 0.001 / Movie #1: 0.001
Minimum - Maximum-0.0000302 - 0.04787388
Average (Standard dev.)0.00086621 (±0.00411965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 712.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.954.954.95
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z712.800712.800712.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-27-15-36
NX/NY/NZ553173
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-0.0000.0480.001

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Supplemental data

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Sample components

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Entire : Baseplate of lactoccocal phage Tuc2009

EntireName: Baseplate of lactoccocal phage Tuc2009
Components
  • Sample: Baseplate of lactoccocal phage Tuc2009
  • Virus: Lactococcus phage Tuc2009 (virus)

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Supramolecule #1000: Baseplate of lactoccocal phage Tuc2009

SupramoleculeName: Baseplate of lactoccocal phage Tuc2009 / type: sample / ID: 1000
Details: The baseplate was selected from images collected from a sample of the entire phages.
Oligomeric state: 6 / Number unique components: 1

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Supramolecule #1: Lactococcus phage Tuc2009

SupramoleculeName: Lactococcus phage Tuc2009 / type: virus / ID: 1 / Name.synonym: Tuc2009 / NCBI-ID: 35241 / Sci species name: Lactococcus phage Tuc2009 / Virus type: OTHER / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Tuc2009
Host (natural)Organism: Lactococcus lactis (lactic acid bacteria) / Strain: UC509.9 / synonym: BACTERIA(EUBACTERIA)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 20 mM Tris-HCL, 10 mM MgSO4, 100 mM NaCl
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 2% w/v uranyl acetate for 20 seconds
GridDetails: 300 mesh copper grid with thin carbon layer, glow discharged for 30 seconds
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 48500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 48500
Sample stageSpecimen holder: Room temperature holder / Specimen holder model: SIDE ENTRY, EUCENTRIC
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateJun 1, 2012
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Number real images: 2000 / Average electron dose: 10 e/Å2 / Details: Images were collected using a 2kx2k CCD camera

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 36.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Spider, Xmipp / Number images used: 2000

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Atomic model buiding 1

Initial modelPDB ID:

4div
PDB Unreleased entry

SoftwareName: Chimera
DetailsThe baseplate was manually fitted and then automatically refined
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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