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The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities.
by single particle reconstruction, at 16.4 A resolution
#1: Surface view with section colored by density value, Surface level: 1.1, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 1.1, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1333 |
|---|---|
| Title | The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. |
| Map | Sixfold averaged tail of bacteriophage K1E |
| Sample | Sixfold averaged tail of bacteriophage K1E |
| Authors | Leiman PG, Battisti AJ, Bowman VD, Stummeyer K, Muhlenhoff M, Gerardy-Schahn R, Scholl D, Molineux IJ |
| Date | Deposition: 2007-03-06, Header release: 2007-03-06, Map release: 2007-07-18, Last update: 2012-10-24 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1.1, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 1.1, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Mol. Biol., Vol. 371, Issue 3, Page 836-49, 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 Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA. |
| Keywords |  Bacterial Capsules (metabolism), Bacteriophages (chemistry), Biological Evolution, Capsid (chemistry), Cryoelectron Microscopy, DNA Packaging, DNA, Viral (chemistry), Escherichia coli (virology), Genome, Viral, Models, Molecular, Sequence Homology, Amino Acid, Species Specificity, Static Electricity, Viral Proteins (chemistry), Virion (chemistry) |
| Links | PII: S0022-2836(07)00756-5, DOI: 10.1016/j.jmb.2007.05.083, PubMed: 17585937 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1333.map ( map file in CCP4 format, 21808 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | float (32-bit) | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 524.48 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.98 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Sixfold averaged tail of bacteriophage K1E | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Sixfold averaged tail of bacteriophage K1E |
|---|---|
| Number of Components | 1 |
| Experimental Mass | 8MDa |
| Theoretical Mass | 8MDa |
| Mass-estimation Method | Primary sequence |
| Component #1: virus - phage K1E tail | |
| Scientific name | Enterobacteria phage K1E |
| Common Name | phage K1E tail |
| Theoretical Mass | 8 MDa |
| Experimental Mass | 8 MDa |
| Details | sixfold averaged |
| Scientific Name of Species | Enterobacteria phage K1E |
| Common Name of Species | phage K1E tail |
| NCBI taxonomy | 344022 |
| Empty | No |
| Enveloped | No |
| Isolate | SPECIES |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 562 Host Species: Escherichia coli Host Category: BACTERIA(EUBACTERIA) |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1 mg/ml |
|---|---|
| Staining | none |
| Specimen Support Details | quantifoil grid |
| Specimen State | particle |
| Buffer | Details: 50 mM Tris HCl pH 7.5, 100 mM NaCl, 8 mM MgSO4 pH: 7.5 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Humidity | 80 |
| Temperature | 300 Kelvin |
| Instrument | FEI VITROBOT |
| Details | Vitrification instrument: Vitrobot |
| Imaging | |
| Microscope | FEI/PHILIPS CM300FEG/T |
| Date | 2005-05-10 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 25 e/A**2 |
| Illumination Mode | SPOT SCAN |
| Lens | |
| Magnification | Nominal: 45000, Calibrated: 47000 |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 700 nm - 3300 nm |
| Specimen Holder | |
| Holder | Side entry liquid nitrogen-cooled cryo specimen holder |
| Model | GATAN LIQUID NITROGEN |
| Temperature | 100 K |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Number of Digital Images | 122 |
| Sampling Size | 7 |
| Quant Bit Number | 12 |
| Scanner | ZEISS SCAI |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | weighted back-projection |
| Software | Spider |
| CTF Correction | Each particle |
| Resolution By Author | 16.4 A |
| Resolution Method | FSC at 0.4 cut-off |
| Single Particle | |
| Number of Projections | 6105 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1333.xml (7.4 KB) | ||
|---|---|---|---|
| Map data | emd_1333.map.gz (13.1 MB) | ||
| Images |  1333.gif (51.3 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1333 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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