+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10926 | |||||||||
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Title | Structure of jumbo coliphage phAPEC6 capsid | |||||||||
Map data | Bacteriophage phAPEC6 capsid at 9A resolution | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Wagemans J / Tsonos J / Holtappels D / Fortuna K / Hernalsteens JP / De Greve H / Estrozi LF / Bacia-Verloop M / Moriscot C / Noben JP ...Wagemans J / Tsonos J / Holtappels D / Fortuna K / Hernalsteens JP / De Greve H / Estrozi LF / Bacia-Verloop M / Moriscot C / Noben JP / Schoehn G / Lavigne R | |||||||||
Citation | Journal: Int J Mol Sci / Year: 2020 Title: Structural Analysis of Jumbo Coliphage phAPEC6. Authors: Jeroen Wagemans / Jessica Tsonos / Dominique Holtappels / Kiandro Fortuna / Jean-Pierre Hernalsteens / Henri De Greve / Leandro F Estrozi / Maria Bacia-Verloop / Christine Moriscot / Jean- ...Authors: Jeroen Wagemans / Jessica Tsonos / Dominique Holtappels / Kiandro Fortuna / Jean-Pierre Hernalsteens / Henri De Greve / Leandro F Estrozi / Maria Bacia-Verloop / Christine Moriscot / Jean-Paul Noben / Guy Schoehn / Rob Lavigne / Abstract: The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI- ...The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI-MS/MS), including the major capsid protein (Gp225; present in 1620 copies), which shows a HK97 capsid protein-based fold. Cryo-electron microscopy experiments showed that the 350-kbp DNA molecule of virus phAPEC6 is packaged in at least 15 concentric layers in the phage capsid. A capsid inner body rod is also present, measuring about 91 nm by 18 nm and oriented along the portal axis. In the phAPEC6 contractile tail, 25 hexameric stacked rings can be distinguished, built of the identified tail sheath protein (Gp277). Cryo-EM reconstruction reveals the base of the unique hairy fibers observed during an initial transmission electron microscopy (TEM) analysis. These very unusual filaments are ordered at three annular positions along the contractile sheath, as well as around the capsid, and may be involved in host interaction. | |||||||||
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_10926.map.gz | 153.8 MB | EMDB map data format | |
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Header (meta data) | emd-10926-v30.xml emd-10926.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd_10926.png | 105.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10926 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10926 | HTTPS FTP |
-Related structure data
Related structure data | 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_10926.map.gz / Format: CCP4 / Size: 515.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bacteriophage phAPEC6 capsid at 9A resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.26 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 : Escherichia coli
Entire | Name: Escherichia coli (E. coli) |
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Components |
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-Supramolecule #1: Escherichia coli
Supramolecule | Name: Escherichia coli / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 562 / Sci species name: Escherichia coli / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Virus shell | Shell ID: 1 / Diameter: 1360.0 Å / T number (triangulation number): 28 |
-Experimental details
-Structure determination
Method | 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 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: Force 1, 2s blotting time. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: KODAK SO-163 FILM / Number grids imaged: 1 / Number real images: 100 / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 6900 |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4149 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |