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- EMDB-1795: The three-dimensional reconstruction of the baseplate of TP901-1 ... -

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Entry
Database: EMDB / ID: EMD-1795
TitleThe three-dimensional reconstruction of the baseplate of TP901-1 bppU mutant
Map dataThe three-dimensional representation of the baseplate of TP901-1 bppU mutant
Sample
  • Sample: TP901-1 bacteriophage bppU mutant
  • Protein or peptide: TP901-1 bppU mutant
KeywordsTP901-1 / bppU / Baseplate / Electron microscopy
Biological speciesLactococcus phage TP901-1 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsBebeacua C / Bron P / Lai L / SkovgaardVegge C / Brondsted L / Spinelli S / Campanacci V / Veesler D / vanHeel M / Cambillau C
CitationJournal: J Biol Chem / Year: 2010
Title: Structure and molecular assignment of lactococcal phage TP901-1 baseplate.
Authors: Cecilia Bebeacua / Patrick Bron / Livia Lai / Christina Skovgaard Vegge / Lone Brøndsted / Silvia Spinelli / Valérie Campanacci / David Veesler / Marin van Heel / Christian Cambillau /
Abstract: P335 lactococcal phages infect the gram(+) bacterium Lactococcus lactis using a large multiprotein complex located at the distal part of the tail and termed baseplate (BP). The BP harbors the ...P335 lactococcal phages infect the gram(+) bacterium Lactococcus lactis using a large multiprotein complex located at the distal part of the tail and termed baseplate (BP). The BP harbors the receptor-binding proteins (RBPs), which allow the specific recognition of saccharidic receptors localized on the host cell surface. We report here the electron microscopic structure of the phage TP901-1 wild-type BP as well as those of two mutants bppL (-) and bppU(-), lacking BppL (the RBPs) or both peripheral BP components (BppL and BppU), respectively. We also achieved an electron microscopic reconstruction of a partial BP complex, formed by BppU and BppL. This complex exhibits a tripod shape and is composed of nine BppLs and three BppUs. These structures, combined with light-scattering measurements, led us to propose that the TP901-1 BP harbors six tripods at its periphery, located around the central tube formed by ORF46 (Dit) hexamers, at its proximal end, and a ORF47 (Tal) trimer at its distal extremity. A total of 54 BppLs (18 RBPs) are thus available to mediate host anchoring with a large apparent avidity. TP901-1 BP exhibits an infection-ready conformation and differs strikingly from the lactococcal phage p2 BP, bearing only 6 RBPs, and which needs a conformational change to reach its activated state. The comparison of several Siphoviridae structures uncovers a close organization of their central BP core whereas striking differences occur at the periphery, leading to diverse mechanisms of host recognition.
History
DepositionSep 25, 2010-
Header (metadata) releaseOct 1, 2010-
Map releaseOct 1, 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: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

tp901-basepl...

Downloads & links

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Map

FileDownload / File: emd_1795.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe three-dimensional representation of the baseplate of TP901-1 bppU mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.64 Å/pix.
x 144 pix.
= 668.16 Å		4.64 Å/pix.
x 144 pix.
= 668.16 Å		4.64 Å/pix.
x 144 pix.
= 668.16 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-3.01994 - 16.2287
Average (Standard dev.)0.0412171 (±0.560903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 668.16 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.644.644.64
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z668.160668.160668.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-3.02016.2290.041

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Supplemental data

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Sample components

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Entire : TP901-1 bacteriophage bppU mutant

EntireName: TP901-1 bacteriophage bppU mutant
Components
  • Sample: TP901-1 bacteriophage bppU mutant
  • Protein or peptide: TP901-1 bppU mutant

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Supramolecule #1000: TP901-1 bacteriophage bppU mutant

SupramoleculeName: TP901-1 bacteriophage bppU mutant / type: sample / ID: 1000 / Oligomeric state: The baseplate is hexameric / Number unique components: 1
Molecular weightExperimental: 1 MDa / Theoretical: 1 MDa

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Macromolecule #1: TP901-1 bppU mutant

MacromoleculeName: TP901-1 bppU mutant / type: protein_or_peptide / ID: 1 / Name.synonym: TP901-1 bppU mutant / Oligomeric state: Hexameric / Recombinant expression: Yes
Source (natural)Organism: Lactococcus phage TP901-1 (virus)
Molecular weightExperimental: 1 MDa / Theoretical: 1 MDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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: 7.5
Details: 100 mM sodium chloride, 10 mM magnesium sulphate, 50 mM Tris pH 7.5, 0.01% (w/v) gelatin
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 2% uranyl acetate for one minute.
GridDetails: Copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Digitization - Sampling interval: 4.64 µm / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsCalibrated magnification: 38000 / Illumination 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

DetailsThe reconstruction was refined using projection matching
CTF correctionDetails: CCD Images
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: IMAGIC
Details: The reconstruction was refined using projection matching
Number images used: 2000
Final angle assignmentDetails: IMAGIC, beta 90 degrees

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