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Yorodumi- EMDB-1333: The structures of bacteriophages K1E and K1-5 explain processive ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1333 | |||||||||
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Title | The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. | |||||||||
Map data | Sixfold averaged tail of bacteriophage K1E | |||||||||
Sample |
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Biological species | Enterobacteria phage K1E (virus) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 16.4 Å | |||||||||
Authors | Leiman PG / Battisti AJ / Bowman VD / Stummeyer K / Muhlenhoff M / Gerardy-Schahn R / Scholl D / Molineux IJ | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1333.map.gz | 13.1 MB | EMDB map data format | |
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Header (meta data) | emd-1333-v30.xml emd-1333.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | 1333.gif | 51.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1333 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1333 | HTTPS FTP |
-Validation report
Summary document | emd_1333_validation.pdf.gz | 261.8 KB | Display | EMDB validaton report |
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Full document | emd_1333_full_validation.pdf.gz | 260.9 KB | Display | |
Data in XML | emd_1333_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1333 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1333 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1333.map.gz / Format: CCP4 / Size: 20.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sixfold averaged tail of bacteriophage K1E | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Sixfold averaged tail of bacteriophage K1E
Entire | Name: Sixfold averaged tail of bacteriophage K1E |
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Components |
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-Supramolecule #1000: Sixfold averaged tail of bacteriophage K1E
Supramolecule | Name: Sixfold averaged tail of bacteriophage K1E / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 8 MDa / Theoretical: 8 MDa / Method: Primary sequence |
-Supramolecule #1: Enterobacteria phage K1E
Supramolecule | Name: Enterobacteria phage K1E / type: virus / ID: 1 / Name.synonym: phage K1E tail / Details: sixfold averaged / 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 tail |
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Host (natural) | Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA) |
Molecular weight | Experimental: 8 MDa / Theoretical: 8 MDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 / Details: 50 mM Tris HCl pH 7.5, 100 mM NaCl, 8 mM MgSO4 |
Staining | Type: NEGATIVE / Details: none |
Grid | Details: quantifoil grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 300 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Temperature | Average: 100 K |
Date | May 10, 2005 |
Image recording | Category: 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.4 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 6105 |