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- EMDB-1336: The structures of bacteriophages K1E and K1-5 explain processive ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1336
TitleThe structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities.
Map dataModel of the complete phage K1E particle
Sample
  • Sample: Complete model of bacteriophage K1E
  • Virus: Enterobacteria phage K1E (virus)
Biological speciesEnterobacteria phage K1E (virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 17.0 Å
AuthorsLeiman PG / Battisti AJ / Bowman VD / Stummeyer K / Muhlenhoff M / Gerardy-Schahn R / Scholl D / Molineux IJ
CitationJournal: J Mol Biol / Year: 2007
Title: The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities.
Authors: Petr G Leiman / Anthony J Battisti / Valorie D Bowman / Katharina Stummeyer / Martina Mühlenhoff / Rita Gerardy-Schahn / Dean Scholl / Ian J Molineux /
Abstract: External polysaccharides of many pathogenic bacteria form capsules protecting the bacteria from the animal immune system and phage infection. However, some bacteriophages can digest these capsules ...External polysaccharides of many pathogenic bacteria form capsules protecting the bacteria from the animal immune system and phage infection. However, some bacteriophages can digest these capsules using glycosidases displayed on the phage particle. We have utilized cryo-electron microscopy to determine the structures of phages K1E and K1-5 and thereby establish the mechanism by which these phages attain and switch their host specificity. Using a specific glycosidase, both phages penetrate the capsule and infect the neuroinvasive human pathogen Escherichia coli K1. In addition to the K1-specific glycosidase, each K1-5 particle carries a second enzyme that allows it to infect E. coli K5, whose capsule is chemically different from that of K1. The enzymes are organized into a multiprotein complex attached via an adapter protein to the virus portal vertex, through which the DNA is ejected during infection. The structure of the complex suggests a mechanism for the apparent processivity of degradation that occurs as the phage drills through the polysaccharide capsule. The enzymes recognize the adapter protein by a conserved N-terminal sequence, providing a mechanism for phages to acquire different enzymes and thus to evolve new host specificities.
History
DepositionMar 7, 2007-
Header (metadata) releaseMar 8, 2007-
Map releaseJul 18, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.601925286
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.601925286
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1336.gif

Downloads & links

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Map

FileDownload / File: emd_1336.map.gz / Format: CCP4 / Size: 68.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationModel of the complete phage K1E particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.47 Å/pix.
x 264 pix.
= 1180.08 Å		4.47 Å/pix.
x 264 pix.
= 1180.08 Å		4.47 Å/pix.
x 264 pix.
= 1180.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.47 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 3.06 / Movie #1: 0.6019253
Minimum - Maximum-1.67512 - 6.04397
Average (Standard dev.)0.0113487 (±0.962804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-132-132-132
Dimensions264264264
Spacing264264264
CellA=B=C: 1180.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.474.474.47
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z1180.0801180.0801180.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-132-132-132
NC/NR/NS264264264
D min/max/mean-1.6756.0440.011

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Supplemental data

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Sample components

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Entire : Complete model of bacteriophage K1E

EntireName: Complete model of bacteriophage K1E
Components
  • Sample: Complete model of bacteriophage K1E
  • Virus: Enterobacteria phage K1E (virus)

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Supramolecule #1000: Complete model of bacteriophage K1E

SupramoleculeName: Complete model of bacteriophage K1E / type: sample / ID: 1000
Details: This is a model of the phage obtained by merging two maps obtained from the same set of particles: 1) Reconstruction of the capsid with 5-fold symmetry imposed; 2) Reconstruction of the tail ...Details: This is a model of the phage obtained by merging two maps obtained from the same set of particles: 1) Reconstruction of the capsid with 5-fold symmetry imposed; 2) Reconstruction of the tail with 6-fold symmetry imposed. The relative orientation of the two maps was found using a lower resolution reconstrution with no symmetry imposed.
Number unique components: 1
Molecular weightExperimental: 58 MDa / Theoretical: 58 MDa / Method: Primary sequence

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Supramolecule #1: Enterobacteria phage K1E

SupramoleculeName: Enterobacteria phage K1E / type: virus / ID: 1 / Name.synonym: phage K1E
Details: The model obtained by combining maps with 5- and 6-fold symmetries imposed
NCBI-ID: 344022 / Sci species name: Enterobacteria phage K1E / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: phage K1E
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 58 MDa / Theoretical: 58 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5 / Details: 50 mM Tris HCl pH 7.5, 100 mM NaCl, 8 mM MgSO4
StainingType: NEGATIVE / Details: no staining
GridDetails: quantifoil grid
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 300 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureAverage: 100 K
DateMay 10, 2005
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 122 / Average electron dose: 25 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.3 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 45000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: Spider, EMAN / Number images used: 6105

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