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- PDB-8edx: Cryo-EM Structure of P74-26 tail-like tubes -

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Basic information

Entry
Database: PDB / ID: 8edx
TitleCryo-EM Structure of P74-26 tail-like tubes
ComponentsTail Tube Protein gp93
KeywordsVIRAL PROTEIN / tail tube protein / bacteriophage
Function / homologyPhage tail tube protein-like / Phage tail tube protein / Uncharacterized protein
Function and homology information
Biological speciesOshimavirus P7426
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsAgnello, E. / Pajak, J. / Liu, X. / Kelch, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817338 United States
National Science Foundation (NSF, United States)2042597 United States
CitationJournal: 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
DepositionSep 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail Tube Protein gp93
B: Tail Tube Protein gp93
C: Tail Tube Protein gp93
D: Tail Tube Protein gp93
E: Tail Tube Protein gp93
F: Tail Tube Protein gp93


Theoretical massNumber of molelcules
Total (without water)227,7346
Polymers227,7346
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Tail Tube Protein gp93


Mass: 37955.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oshimavirus P7426 / Gene: P74p93 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress (DE3) / References: UniProt: A7XXS2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: In vitro-assembled tail-like tubes of tail tube protein gp93
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Oshimavirus P7426
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: ArcticExpress (DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2300 mMPotassium ChlorideKCl1
320 mMImidazoleC3H4N21
45 mMBeta-mercaptoethanol2-MercaptoethanolC2H6OS1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grids were glow discharged at 25 mA for 60 sec with negative polarity.
Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 38.4312 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
4CTFFINDCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -44 ° / Axial rise/subunit: 40 Å / Axial symmetry: C3
Particle selectionNum. of particles selected: 619907
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 395357 / Num. of class averages: 1 / Symmetry type: HELICAL

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