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- EMDB-1620: Three-dimensional Structure of Tropism-Switching Bordetella Bacte... -

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Basic information

Entry
Database: EMDB / ID: EMD-1620
TitleThree-dimensional Structure of Tropism-Switching Bordetella Bacteriophage
Map data2f 3D map of phage
Sample
  • Sample: Bordetella Bacteriophage
  • Virus: Bordetella phage BPP-1 (virus)
KeywordscryoEM / cryo-electron microscopy / BPP / Bordetella plus phage
Biological speciesBordetella phage BPP-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 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 9, 2009-
Header (metadata) releaseMay 26, 2009-
Map releaseMar 3, 2010-
UpdateOct 31, 2012-
Current statusOct 31, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1620.png

Downloads & links

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Map

FileDownload / File: emd_1620.map.gz / Format: CCP4 / Size: 881.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2f 3D map of phage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 390 pix.
= 379.936 Å		0.97 Å/pix.
x 779 pix.
= 756.9 Å		0.97 Å/pix.
x 779 pix.
= 756.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.97163 Å / Y: 0.97163 Å / Z: 0.9742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-7.77282 - 10.407299999999999
Average (Standard dev.)0.0813415 (±1.22751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions779779390
Spacing779779390
CellA: 756.9 Å / B: 756.9 Å / C: 379.936 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.971630295250320.971630295250320.97419487179487
M x/y/z779779390
origin x/y/z0.0000.0000.000
length x/y/z756.900756.900379.936
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS779779390
D min/max/mean-7.77310.4070.081

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Supplemental data

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Sample components

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Entire : Bordetella Bacteriophage

EntireName: Bordetella Bacteriophage
Components
  • Sample: Bordetella Bacteriophage
  • Virus: Bordetella phage BPP-1 (virus)

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Supramolecule #1000: Bordetella Bacteriophage

SupramoleculeName: Bordetella Bacteriophage / type: sample / ID: 1000 / Oligomeric state: icosahedral particle of whole virus / 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: Bordetella Bacteriophage / NCBI-ID: 194699 / Sci species name: Bordetella phage BPP-1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Bordetella Bacteriophage
Host (natural)Organism: Bordetella (bacteria) / synonym: BACTERIA(EUBACTERIA)

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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

VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: lab-made plunger. Vitrification was carried out at room temperature. CPV were embedded in a thin layer of vitreous ice suspended across the holes of holey carbon ...Details: Vitrification instrument: lab-made plunger. Vitrification was carried out at room temperature. CPV were embedded in a thin layer of vitreous ice suspended across the holes of holey carbon films for cryoEM imaging.
Method: blot for 3 seconds with filter paper before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 154380 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 154380
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS / Average electron dose: 20 e/Å2
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMIRS
Details: Determination of particle orientation and center parameters and subsequent 3D reconstruction were carried out using programs in the IMIRS software package, which are based on Fourier common ...Details: Determination of particle orientation and center parameters and subsequent 3D reconstruction were carried out using programs in the IMIRS software package, which are based on Fourier common lines and Fourier-Bessel synthesis methods.
Number images used: 9000

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