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- EMDB-1706: Cryo-EM map of Lactococcal phage p2 baseplate consisting of ORF 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-1706
TitleCryo-EM map of Lactococcal phage p2 baseplate consisting of ORF 15, 16 and 18.
Map dataCryo-EM map of p2 phage baseplate
Sample
  • Sample: Over-expressed Lactococcal phage p2 baseplate
  • Protein or peptide: p2 Lactoccocal phage baseplate
KeywordsBaseplate / phage / P2 / Siphoviridae / orf 15 / orf 16 / orf 18 / RBP / cryo-EM
Biological speciesLactococcus lactis phage p2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 26.0 Å
AuthorsSciara G / Bebeacua C / Bron P / Tremblay D / Ortiz-Lombardia M / Lichiere J / Van Heel M / Campanacci V / Moineau S / Cambillau C
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Structure of lactococcal phage p2 baseplate and its mechanism of activation.
Authors: Giuliano Sciara / Cecilia Bebeacua / Patrick Bron / Denise Tremblay / Miguel Ortiz-Lombardia / Julie Lichière / Marin van Heel / Valérie Campanacci / Sylvain Moineau / Christian Cambillau /
Abstract: Siphoviridae is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+ Lactococcus lactis possess a baseplate at the tip of their ...Siphoviridae is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+ Lactococcus lactis possess a baseplate at the tip of their tail involved in host recognition and attachment. Here, we report analysis of the p2 phage baseplate structure by X-ray crystallography and electron microscopy and propose a mechanism for the baseplate activation during attachment to the host cell. This approximately 1 MDa, Escherichia coli-expressed baseplate is composed of three protein species, including six trimers of the receptor-binding protein (RBP). RBPs host-recognition domains point upwards, towards the capsid, in agreement with the electron-microscopy map of the free virion. In the presence of Ca(2+), a cation mandatory for infection, the RBPs rotated 200 degrees downwards, presenting their binding sites to the host, and a channel opens at the bottom of the baseplate for DNA passage. These conformational changes reveal a novel siphophage activation and host-recognition mechanism leading ultimately to DNA ejection.
History
DepositionMar 3, 2010-
Header (metadata) releaseSep 3, 2010-
Map releaseSep 3, 2010-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0308
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0308
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1706.png

Downloads & links

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Map

FileDownload / File: emd_1706.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of p2 phage baseplate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.37 Å/pix.
x 130 pix.
= 568.1 Å		4.37 Å/pix.
x 130 pix.
= 568.1 Å		4.37 Å/pix.
x 130 pix.
= 568.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0308 / Movie #1: 0.0308
Minimum - Maximum-0.124622 - 0.142966
Average (Standard dev.)0.000648796 (±0.00774832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions130130130
Spacing130130130
CellA=B=C: 568.1 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.374.374.37
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z568.100568.100568.100
α/β/γ90.00090.00090.000
start NX/NY/NZ-61-61-60
NX/NY/NZ122122122
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
D min/max/mean-0.1250.1430.001

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Supplemental data

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Sample components

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Entire : Over-expressed Lactococcal phage p2 baseplate

EntireName: Over-expressed Lactococcal phage p2 baseplate
Components
  • Sample: Over-expressed Lactococcal phage p2 baseplate
  • Protein or peptide: p2 Lactoccocal phage baseplate

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Supramolecule #1000: Over-expressed Lactococcal phage p2 baseplate

SupramoleculeName: Over-expressed Lactococcal phage p2 baseplate / type: sample / ID: 1000
Oligomeric state: One homotrimer of ORF16 binds to two hexamers of ORF15 and binds to six homotrimers of ORF18
Number unique components: 1
Molecular weightExperimental: 1 MDa

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Macromolecule #1: p2 Lactoccocal phage baseplate

MacromoleculeName: p2 Lactoccocal phage baseplate / type: protein_or_peptide / ID: 1 / Name.synonym: p2 baseplate / Details: Complexes was cross-linked by glutaraldehyde / Recombinant expression: Yes
Source (natural)Organism: Lactococcus lactis phage p2 (virus)
Molecular weightExperimental: 1 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: Gateway pDEST14

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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

Concentration0.07 mg/mL
BufferpH: 7.5 / Details: 10mM HEPES, 150mM NaCl, 0.02% Glutaraldehyde
GridDetails: R2.2 Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 92 % / Chamber temperature: 103.15 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Vitrification instrument: CP3 Gatan / Method: Blot for 1 second before plunging

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureAverage: 98.15 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 10 µm / Number real images: 46 / Average electron dose: 18 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45710 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC V
Final angle assignmentDetails: beta 0 degrees, gamma 90
Final two d classificationNumber classes: 263

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