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- EMDB-1792: EM map of TP901-1 BppU-BppL complex -

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Basic information

Entry
Database: EMDB / ID: EMD-1792
TitleEM map of TP901-1 BppU-BppL complex
Map dataEM map of TP9101-1 BppU-BppL complex
Sample
  • Sample: BppU/BppL complex from Lactococcal Phage TP901-1
  • Protein or peptide: BppU
  • Protein or peptide: BppL
KeywordsBacteriophage / TP9101-1 / BppU / BppL / ORF 48 / ORF 49
Biological speciesLactococcus phage TP901-1 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 24.8 Å
AuthorsBron P
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 23, 2010-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
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: 15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1792.png

Downloads & links

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Map

FileDownload / File: emd_1792.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of TP9101-1 BppU-BppL complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 90 pix.
= 360. Å		4 Å/pix.
x 90 pix.
= 360. Å		4 Å/pix.
x 90 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 15.0 / Movie #1: 15
Minimum - Maximum-26.59852982 - 85.599136349999995
Average (Standard dev.)0.0 (±5.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-44-45-45
Dimensions909090
Spacing909090
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z360.000360.000360.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-45-44-45
NC/NR/NS909090
D min/max/mean-26.59985.5990.000

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Supplemental data

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Sample components

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Entire : BppU/BppL complex from Lactococcal Phage TP901-1

EntireName: BppU/BppL complex from Lactococcal Phage TP901-1
Components
  • Sample: BppU/BppL complex from Lactococcal Phage TP901-1
  • Protein or peptide: BppU
  • Protein or peptide: BppL

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Supramolecule #1000: BppU/BppL complex from Lactococcal Phage TP901-1

SupramoleculeName: BppU/BppL complex from Lactococcal Phage TP901-1 / type: sample / ID: 1000
Oligomeric state: one trimer of BppU and three trimers of BppL
Number unique components: 2

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Macromolecule #1: BppU

MacromoleculeName: BppU / type: protein_or_peptide / ID: 1 / Name.synonym: ORF48 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Lactococcus phage TP901-1 (virus)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #2: BppL

MacromoleculeName: BppL / type: protein_or_peptide / ID: 2 / Name.synonym: ORF49 / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Lactococcus phage TP901-1 (virus)
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

Concentration0.05 mg/mL
BufferpH: 7.5 / Details: 10 mM Hepes, 150 mM NaCl, 1 mM PMSF
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 1% uranyl acetate for 1 min.
GridDetails: 400 mesh cupper griid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2200FS
Alignment procedureLegacy - Astigmatism: Astigmatism was corrected at 150,000 times magnification
Specialist opticsEnergy filter - Name: Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DetailsLow-dose imaging
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: 8 / Average electron dose: 18 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC V / Number images used: 8314

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Atomic model buiding 1

Initial modelPDB ID:

2f0c

DetailsThe trimers were separately fitted by manual docking and refined using the docking program integrated into Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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