+Open data
-Basic information
Entry | Database: PDB / ID: 8ed0 | |||||||||
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Title | Cryo-EM Structure of the P74-26 Tail Tube | |||||||||
Components | Tail Tube Protein gp93 | |||||||||
Keywords | VIRAL PROTEIN / tail tube protein / bacteriophage | |||||||||
Function / homology | Phage tail tube protein-like / Phage tail tube protein / Major capsid protein Function and homology information | |||||||||
Biological species | Oshimavirus P7426 | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.72 Å | |||||||||
Authors | Agnello, E. / Pajak, J. / Liu, X. / Kelch, B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J Biol Chem / Year: 2023 Title: Conformational dynamics control assembly of an extremely long bacteriophage tail tube. Authors: Emily Agnello / Joshua Pajak / Xingchen Liu / Brian A Kelch / Abstract: Tail tube assembly is an essential step in the lifecycle of long-tailed bacteriophages. Limited structural and biophysical information has impeded an understanding of assembly and stability of their ...Tail tube assembly is an essential step in the lifecycle of long-tailed bacteriophages. Limited structural and biophysical information has impeded an understanding of assembly and stability of their long, flexible tail tubes. The hyperthermophilic phage P74-26 is particularly intriguing as it has the longest tail of any known virus (nearly 1 μm) and is the most thermostable known phage. Here, we use structures of the P74-26 tail tube along with an in vitro system for studying tube assembly kinetics to propose the first molecular model for the tail tube assembly of long-tailed phages. Our high-resolution cryo-EM structure provides insight into how the P74-26 phage assembles through flexible loops that fit into neighboring rings through tight "ball-and-socket"-like interactions. Guided by this structure, and in combination with mutational, light scattering, and molecular dynamics simulations data, we propose a model for the assembly of conserved tube-like structures across phage and other entities possessing tail tube-like proteins. We propose that formation of a full ring promotes the adoption of a tube elongation-competent conformation among the flexible loops and their corresponding sockets, which is further stabilized by an adjacent ring. Tail assembly is controlled by the cooperative interaction of dynamic intraring and interring contacts. Given the structural conservation among tail tube proteins and tail-like structures, our model can explain the mechanism of high-fidelity assembly of long, stable tubes. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ed0.cif.gz | 384.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ed0.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ed0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ed0_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8ed0_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ed0_validation.xml.gz | 62.4 KB | Display | |
Data in CIF | 8ed0_validation.cif.gz | 85.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/8ed0 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/8ed0 | HTTPS FTP |
-Related structure data
Related structure data | 28026MC 8edxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 37955.738 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXS2 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Oshimavirus P7426 / Type: VIRUS / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Oshimavirus P7426 | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Thermus thermophilus | ||||||||||||||||||||
Virus shell | Triangulation number (T number): 7 | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Specimen concentration = 1 x 10^10 PFU/mL | ||||||||||||||||||||
Specimen support | Details: Grids were glow discharged at 25 mA for 60 sec with negative polarity. Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 37.9644 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2127 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -44 ° / Axial rise/subunit: 40 Å / Axial symmetry: C3 | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 795534 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 787734 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |