+Open data
-Basic information
Entry | Database: PDB / ID: 5w5f | |||||||||
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Title | Cryo-EM structure of the T4 tail tube | |||||||||
Components | Tail tube protein gp19 | |||||||||
Keywords | VIRAL PROTEIN / T4 tail tube / dose limit / helical reconstruction | |||||||||
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 Function and homology information | |||||||||
Biological species | Enterobacteria phage T4 sensu lato (virus) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Zheng, W. / Wang, F. / Taylor, N.M. / Guerrero-Ferreira, R.C. / Leiman, P.G. / Egelman, E.H. | |||||||||
Funding support | United States, Switzerland, 2items
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Citation | Journal: Structure / Year: 2017 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5w5f.cif.gz | 500.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w5f.ent.gz | 420.4 KB | Display | PDB format |
PDBx/mmJSON format | 5w5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w5f_validation.pdf.gz | 985.4 KB | Display | wwPDB validaton report |
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Full document | 5w5f_full_validation.pdf.gz | 1011.3 KB | Display | |
Data in XML | 5w5f_validation.xml.gz | 75 KB | Display | |
Data in CIF | 5w5f_validation.cif.gz | 95.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/5w5f ftp://data.pdbj.org/pub/pdb/validation_reports/w5/5w5f | HTTPS FTP |
-Related structure data
Related structure data | 8767MC 5w5eC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 4 / Rise per n subunits: 40.2 Å / Rotation per n subunits: 18.2 °) |
-Components
#1: Protein | Mass: 18479.613 Da / Num. of mol.: 18 / Source method: isolated from a natural source Source: (natural) Enterobacteria phage T4 sensu lato (virus) References: UniProt: P13333 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Enterobacteria phage T4 sensu lato (virus) |
Buffer solution | pH: 8 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: Gatan image filter |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 18.2 ° / Axial rise/subunit: 40.2 Å / Axial symmetry: C6 | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 26320 | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26320 / Symmetry type: HELICAL | |||||||||||||||||||||||||||
Atomic model building | Space: REAL | |||||||||||||||||||||||||||
Refine LS restraints |
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