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- EMDB-1619: Three-dimensional Structure of Tropism-Switching Bordetella Bacte... -

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Basic information

Entry
Database: EMDB / ID: EMD-1619
TitleThree-dimensional Structure of Tropism-Switching Bordetella Bacteriophage
Map dataBottom view of the BPP-1 phage particle (after average)
Sample
  • Sample: Bvg plus tropic phage-1 (BPP-1) bacteriophage
  • Virus: Bordetella phage BPP-1 (virus)
Keywordscryo-electron tomography / Bordetella plus phage / major tropism determinant
Biological speciesBordetella phage BPP-1 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
AuthorsDai W / Hodes A / Hui WH / Gingery M / Miller JF / Zhou ZH
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Three-dimensional structure of tropism-switching Bordetella bacteriophage.
Authors: Wei Dai / Asher Hodes / Wong H Hui / Mari Gingery / Jeff F Miller / Z Hong Zhou /
Abstract: Bacteriophage BPP-1, which infects Bordetella species, can switch its specificity by mutations to the ligand-binding surface of its major tropism-determinant protein, Mtd. This targeted mutagenesis ...Bacteriophage BPP-1, which infects Bordetella species, can switch its specificity by mutations to the ligand-binding surface of its major tropism-determinant protein, Mtd. This targeted mutagenesis results from the activity of a phage-encoded diversity-generating retroelement. Purified Mtd binds its receptor with low affinity, yet BPP-1 binding and infection of Bordettella cells are efficient because of high-avidity binding between phage-associated Mtd and its receptor. Here, using an integrative approach of three-dimensional (3D) structural analyses of the entire phage by cryo-electron tomography and single-prticle cryo-electron microscopy, we provide direct localization of Mtd in the phage and the structural basis of the high-avidity binding of the BPP-1 phage. Our structure shows that each BPP-1 particle has a T = 7 icosahedral head and an unusual tail apparatus consisting of a short central tail "hub," six short tail spikes, and six extended tail fibers. Subtomographic averaging of the tail fiber maps revealed a two-lobed globular structure at the distal end of each long tail fiber. Tomographic reconstructions of immuno-gold-labeled BPP-1 directly localized Mtd to these globular structures. Finally, our icosahedral reconstruction of the BPP-1 head at 7A resolution reveals an HK97-like major capsid protein stabilized by a smaller cementing protein. Our structure represents a unique bacteriophage reconstruction with its tail fibers and ligand-binding domains shown in relation to its tail apparatus. The localization of Mtd at the distal ends of the six tail fibers explains the high avidity binding of Mtd molecules to cell surfaces for initiation of infection.
History
DepositionMay 5, 2009-
Header (metadata) releaseMay 20, 2009-
Map releaseMar 3, 2010-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1619.png

Downloads & links

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Map

FileDownload / File: emd_1619.map.gz / Format: CCP4 / Size: 8.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBottom view of the BPP-1 phage particle (after average)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.86 Å/pix.
x 160 pix.
= 1257.6 Å		7.86 Å/pix.
x 120 pix.
= 943.2 Å		7.86 Å/pix.
x 120 pix.
= 943.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 14.4
Minimum - Maximum-106.010999999999996 - 108.215000000000003
Average (Standard dev.)-10.1366 (±22.092500000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-80
Dimensions120120160
Spacing120120160
CellA: 943.2 Å / B: 943.2 Å / C: 1257.6 Å
α=β=γ: 90 °

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Supplemental data

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Sample components

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Entire : Bvg plus tropic phage-1 (BPP-1) bacteriophage

EntireName: Bvg plus tropic phage-1 (BPP-1) bacteriophage
Components
  • Sample: Bvg plus tropic phage-1 (BPP-1) bacteriophage
  • Virus: Bordetella phage BPP-1 (virus)

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Supramolecule #1000: Bvg plus tropic phage-1 (BPP-1) bacteriophage

SupramoleculeName: Bvg plus tropic phage-1 (BPP-1) bacteriophage / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Bordetella phage BPP-1

SupramoleculeName: Bordetella phage BPP-1 / type: virus / ID: 1 / Name.synonym: BPP-1 bacteriophage / NCBI-ID: 194699 / Sci species name: Bordetella phage BPP-1 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: BPP-1 bacteriophage
Host (natural)Organism: Bordetella (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 680 Å / T number (triangulation number): 7

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

GridDetails: 200 mesh grid
VitrificationCryogen name: ETHANE / Instrument: OTHER / Method: Blot for 1 second before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 23000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 °
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 40.0 Å / Software - Name: ProTomo / Details: Final map was averaged from 60 particles

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