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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8767 | |||||||||
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Title | Cryo-EM structure of the T4 tail tube | |||||||||
![]() | Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament | |||||||||
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![]() | T4 tail tube / dose limit / helical reconstruction / VIRAL PROTEIN | |||||||||
Function / homology | symbiont genome ejection through host cell envelope, contractile tail mechanism / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / virus tail, tube / structural molecule activity / Tail tube protein gp19![]() | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Zheng W / Wang F | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Refined Cryo-EM Structure of the T4 Tail Tube: Exploring the Lowest Dose Limit. Authors: Weili Zheng / Fengbin Wang / Nicholas M I Taylor / Ricardo C Guerrero-Ferreira / Petr G Leiman / Edward H Egelman / ![]() ![]() Abstract: The bacteriophage T4 contractile tail (containing a tube and sheath) was the first biological assembly reconstructed in three dimensions by electron microscopy at a resolution of ∼35 Å in 1968. A ...The bacteriophage T4 contractile tail (containing a tube and sheath) was the first biological assembly reconstructed in three dimensions by electron microscopy at a resolution of ∼35 Å in 1968. A single-particle reconstruction of the T4 baseplate was able to generate a 4.1 Å resolution map for the first two rings of the tube using the overall baseplate for alignment. We have now reconstructed the T4 tail tube at a resolution of 3.4 Å, more than a 1,000-fold increase in information content for the tube from 1968. We have used legacy software (Spider) to show that we can do better than the typical 2/3 Nyquist frequency. A reasonable map can be generated with only 1.5 electrons/Å using the higher dose images for alignment, but increasing the dose results in a better map, consistent with other reports that electron dose does not represent the main limitation on resolution in cryo-electron microscopy. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.9 KB 10.9 KB | Display Display | ![]() |
Images | ![]() | 318 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 473.7 KB | Display | ![]() |
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Full document | ![]() | 473.3 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w5fMC ![]() 5w5eC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament
Entire | Name: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament |
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Components |
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-Supramolecule #1: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament
Supramolecule | Name: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Tail tube protein gp19
Macromolecule | Name: Tail tube protein gp19 / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 18.479613 KDa |
Sequence | String: MFVDDVTRAF ESGDFARPNL FQVEISYLGQ NFTFQCKATA LPAGIVEKIP VGFMNRKINV AGDRTFDDWT VTVMNDEAHD ARQKFVDWQ SIAAGQGNEI TGGKPAEYKK SAIVRQYARD AKTVTKEIEI KGLWPTNVGE LQLDWDSNNE IQTFEVTLAL D YWE UniProtKB: Tail tube protein gp19 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: Gatan image filter |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 40.2 Å Applied symmetry - Helical parameters - Δ&Phi: 18.2 ° Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 26320 |
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Segment selection | Number selected: 26320 / Software - Name: EMAN2 |
Startup model | Type of model: NONE / Details: featureless cylinder |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: SPIDER |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-5w5f: |