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- EMDB-1699: Structure of Lactococcal Phage p2 Baseplate and its Mechanism of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1699
TitleStructure of Lactococcal Phage p2 Baseplate and its Mechanism of Activation
Map dataThis is the ccp4 file of the EM 3D reconstruction of the baseplate of the wild-type p2 bacteriophage. The map is associated to the following PDB entries: PDB: 2WZP: BP closed form PDB: 2X53: BP Activated form C2 PDB: 2X54 + 2X5A: BP Activated form P2
Sample
  • Sample: P2 baseplate wild-type
  • Protein or peptide: P2 baseplate
Keywordsp2 / baseplate / phage / EM
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / virus tail / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Phage tail base-plate attachment protein ORF16 / Baseplate protein Gp15-like / Baseplate protein Gp16, domain D4 / Baseplate protein Gp16, domain 1 and 2 / : / : / : / : / Distal tail protein, N-terminal domain / Phage tail base-plate attachment protein N-terminal barrel domain ...Phage tail base-plate attachment protein ORF16 / Baseplate protein Gp15-like / Baseplate protein Gp16, domain D4 / Baseplate protein Gp16, domain 1 and 2 / : / : / : / : / Distal tail protein, N-terminal domain / Phage tail base-plate attachment protein N-terminal barrel domain / Phage tail base-plate attachment protein C-terminal insertion domain / Phage tail base-plate attachment protein N0 domain / Phage tail base-plate attachment protein C-terminal barrel domain / Dit, C-terminal domain / : / Lactococcus phage p2, Receptor binding protein, neck domain / : / Lactophage receptor-binding protein N-terminal shoulder domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
Baseplate protein gp16 / Distal tail protein / Receptor binding protein
Similarity search - Component
Biological speciesLactococcus phage p2 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 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
DepositionFeb 5, 2010-
Header (metadata) releaseMar 10, 2010-
Map releaseMar 10, 2010-
UpdateJun 1, 2010-
Current statusJun 1, 2010Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zjj
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zjj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

3d_p2basepla...

Downloads & links

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Map

FileDownload / File: emd_1699.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the ccp4 file of the EM 3D reconstruction of the baseplate of the wild-type p2 bacteriophage. The map is associated to the following PDB entries: PDB: 2WZP: BP closed form PDB: 2X53: BP Activated form C2 PDB: 2X54 + 2X5A: BP Activated form P2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.64 Å/pix.
x 128 pix.
= 593.92 Å		4.64 Å/pix.
x 128 pix.
= 593.92 Å		4.64 Å/pix.
x 128 pix.
= 593.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-7.12447 - 15.0054
Average (Standard dev.)0.0791262 (±0.812704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-63-64
Dimensions128128128
Spacing128128128
CellA=B=C: 593.92 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.644.644.64
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z593.920593.920593.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-63-64-64
NC/NR/NS128128128
D min/max/mean-7.12415.0050.079

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Supplemental data

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Sample components

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Entire : P2 baseplate wild-type

EntireName: P2 baseplate wild-type
Components
  • Sample: P2 baseplate wild-type
  • Protein or peptide: P2 baseplate

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Supramolecule #1000: P2 baseplate wild-type

SupramoleculeName: P2 baseplate wild-type / type: sample / ID: 1000 / Oligomeric state: Homohexamer / Number unique components: 1
Molecular weightExperimental: 1 MDa / Theoretical: 1 MDa

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Macromolecule #1: P2 baseplate

MacromoleculeName: P2 baseplate / type: protein_or_peptide / ID: 1 / Name.synonym: P2 baseplate / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: No
Source (natural)Organism: Lactococcus phage p2 (virus)

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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

StainingType: NEGATIVE
Details: Sample was incubated on glow-discharged grid for approximately one minute. 2% uranyl acetate was applied onto the sample and left for about 30 seconds.
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/UT
Alignment procedureLegacy - Astigmatism: corrected at 200,000 times magnification
Image recordingDigitization - Sampling interval: 2.32 µm / Number real images: 1000 / Average electron dose: 10 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Room Temperature / Specimen holder model: OTHER

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Image processing

CTF correctionDetails: CCD Images
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: OTHER / Software - Name: IMAGIC-5
Details: Initial map calculated with class averages. Final map calculated after projection matching refinement.
Number images used: 9486
Final angle assignmentDetails: IMAGIC

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