+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5331 | |||||||||
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Title | The cryoEM structure of the bacteriophage phiKZ polysheath | |||||||||
Map data | This is a map of the bacteriophage phiKZ polysheath | |||||||||
Sample |
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Keywords | homopolymer of the bacteriophage tail sheath protein | |||||||||
Function / homology | : / Bacteriophage phiKZ, gp29PR / PHIKZ029 Function and homology information | |||||||||
Biological species | Pseudomonas phage phiKZ (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 19.0 Å | |||||||||
Authors | Aksyuk AA / Kurochkina LP / Fokine A / Mesyanzhinov VV / Rossmann MG | |||||||||
Citation | Journal: Structure / Year: 2011 Title: Structural conservation of the myoviridae phage tail sheath protein fold. Authors: Anastasia A Aksyuk / Lidia P Kurochkina / Andrei Fokine / Farhad Forouhar / Vadim V Mesyanzhinov / Liang Tong / Michael G Rossmann / Abstract: Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The ...Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 Å diameter icosahedral head and a 2000 Å-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 Å resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 Å resolution. Despite low sequence identity between these proteins, all of these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4. | |||||||||
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_5331.map.gz | 39.2 MB | EMDB map data format | |
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Header (meta data) | emd-5331-v30.xml emd-5331.xml | 7.1 KB 7.1 KB | Display Display | EMDB header |
Images | emd_5331.jpg | 979.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5331 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5331 | HTTPS FTP |
-Validation report
Summary document | emd_5331_validation.pdf.gz | 334.8 KB | Display | EMDB validaton report |
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Full document | emd_5331_full_validation.pdf.gz | 334.3 KB | Display | |
Data in XML | emd_5331_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5331 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5331 | HTTPS FTP |
-Related structure data
Related structure data | 3j0iMC 5332C 3j0hC 3speC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5331.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map of the bacteriophage phiKZ polysheath | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.49 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 polysheath
Entire | Name: Bacteriophage phiKZ polysheath |
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Components |
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-Supramolecule #1000: Bacteriophage phiKZ polysheath
Supramolecule | Name: Bacteriophage phiKZ polysheath / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: bacteriophage phiKZ polysheaths
Macromolecule | Name: bacteriophage phiKZ polysheaths / type: protein_or_peptide / ID: 1 / Name.synonym: polysheaths / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: Pseudomonas phage phiKZ (virus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER |
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