+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1415 | |||||||||
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Title | Cryo-EM study of the Pseudomonas bacteriophage phiKZ. | |||||||||
Map data | This is a 3D model of the bacteriophage phiKZ based on the previously deposited reconstructions of the capsid (EMD-1392) and the tail (EMD-1393) | |||||||||
Sample |
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Biological species | Pseudomonas phage phiKZ (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 28.0 Å | |||||||||
Authors | Fokine A / Battisti A / Bowman V / Efimov A / Kurochkina L / Chipman P / Mesyanzhinov V / Rossmann M | |||||||||
Citation | Journal: Structure / Year: 2007 Title: Cryo-EM study of the Pseudomonas bacteriophage phiKZ. Authors: Andrei Fokine / Anthony J Battisti / Valorie D Bowman / Andrei V Efimov / Lidia P Kurochkina / Paul R Chipman / Vadim V Mesyanzhinov / Michael G Rossmann / Abstract: The phiKZ virus is one of the largest known bacteriophages. It infects Pseudomonas aeruginosa, which is frequently pathogenic in humans, and, therefore, has potential for phage therapy. The phiKZ ...The phiKZ virus is one of the largest known bacteriophages. It infects Pseudomonas aeruginosa, which is frequently pathogenic in humans, and, therefore, has potential for phage therapy. The phiKZ virion consists of an approximately 1450 A diameter icosahedral head and an approximately 2000 A long contractile tail. The structure of the phiKZ tail has been determined using cryo-electron microscopy. The phiKZ tail is much longer than that of bacteriophage T4. However, the helical parameters of their contractile sheaths, surrounding their tail tubes, are comparable. Although there is no recognizable sequence similarity between the phiKZ and T4 tail sheath proteins, they are similar in size and shape, suggesting that they evolved from a common ancestor. The phiKZ baseplate is significantly larger than that of T4 and has a flatter shape. Nevertheless, phiKZ, similar to T4, has a cell-puncturing device in the middle of its baseplate. | |||||||||
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_1415.map.gz | 12.3 MB | EMDB map data format | |
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Header (meta data) | emd-1415-v30.xml emd-1415.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | 1415.gif | 35.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1415 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1415 | HTTPS FTP |
-Validation report
Summary document | emd_1415_validation.pdf.gz | 202.9 KB | Display | EMDB validaton report |
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Full document | emd_1415_full_validation.pdf.gz | 202 KB | Display | |
Data in XML | emd_1415_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1415 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1415 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1415.map.gz / Format: CCP4 / Size: 48.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a 3D model of the bacteriophage phiKZ based on the previously deposited reconstructions of the capsid (EMD-1392) and the tail (EMD-1393) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.4848 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 : Bacteriophage phiKZ
Entire | Name: Bacteriophage phiKZ |
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Components |
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-Supramolecule #1000: Bacteriophage phiKZ
Supramolecule | Name: Bacteriophage phiKZ / type: sample / ID: 1000 / Oligomeric state: one / Number unique components: 1 |
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-Supramolecule #1: Pseudomonas phage phiKZ
Supramolecule | Name: Pseudomonas phage phiKZ / type: virus / ID: 1 / NCBI-ID: 169683 / Sci species name: Pseudomonas phage phiKZ / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Pseudomonas aeruginosa (bacteria) / synonym: BACTERIA(EUBACTERIA) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 50 mM tris-Acetate-EDTA buffer (pH 7.5) |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 40 % / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: in house manufactured / Method: hand blot 3 seconds, plugging during blot |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Alignment procedure | Legacy - Astigmatism: live fft |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 112 / Average electron dose: 20 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 33200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 33000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER Details: This is a model of the phiKZ virion based on the previously deposited reconstructions of the phiKZ capsid and the tail part. |
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