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- EMDB-28042: Cryo-EM Structure of P74-26 tail-like tubes -

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Basic information

Entry
Database: EMDB / ID: EMD-28042
TitleCryo-EM Structure of P74-26 tail-like tubes
Map data
Sample
  • Complex: In vitro-assembled tail-like tubes of tail tube protein gp93
    • Protein or peptide: Tail Tube Protein gp93
Keywordstail tube protein / bacteriophage / VIRAL PROTEIN
Function / homologyPhage tail tube protein-like / Phage tail tube protein / Major capsid protein
Function and homology information
Biological speciesOshimavirus P7426
Methodhelical reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsAgnello E / Pajak J / Liu X / Kelch B
Funding support United States, 2 items
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, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28042.png

Downloads & links

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Map

FileDownload / File: emd_28042.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.87 Å
Density
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.257862 - 4.233602
Average (Standard dev.)0.0066041714 (±0.1923028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28042_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28042_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In vitro-assembled tail-like tubes of tail tube protein gp93

EntireName: In vitro-assembled tail-like tubes of tail tube protein gp93
Components
  • Complex: In vitro-assembled tail-like tubes of tail tube protein gp93
    • Protein or peptide: Tail Tube Protein gp93

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Supramolecule #1: In vitro-assembled tail-like tubes of tail tube protein gp93

SupramoleculeName: In vitro-assembled tail-like tubes of tail tube protein gp93
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oshimavirus P7426

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Macromolecule #1: Tail Tube Protein gp93

MacromoleculeName: Tail Tube Protein gp93 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 37.955738 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRGVDTFLAF KEQADLKTPA TLASLAAGDF LAFNSESLSG RQQVIQSRAI RRMPMRQIAY TANGTVEAGG AVEFTTSNYV LKKLLPLIF HSKTGQEDDP DGDGATFTLV NGGVLTPFTA FVGFDGPEGK YVRRFFGAKV NQATFSARVN DMLNLNLDVQ A IGKDILQP ...String:
MRGVDTFLAF KEQADLKTPA TLASLAAGDF LAFNSESLSG RQQVIQSRAI RRMPMRQIAY TANGTVEAGG AVEFTTSNYV LKKLLPLIF HSKTGQEDDP DGDGATFTLV NGGVLTPFTA FVGFDGPEGK YVRRFFGAKV NQATFSARVN DMLNLNLDVQ A IGKDILQP GDPGWVNVTP VYPGGDEEYA YVFYQARVLI KAGDMADLAE LPVESFDLTI NHNLNTNRYR LGSIYRQSLD EG VTEVTGT FTLDAAVKSI SGPALNLTGG TAHDPAFLEK VALYGKYAAL KLEFIDPTRE VAEGVPCRLT IHLPFVRLEE PDF QVRDPG VITGSARFNA YETISVTHVA KF

UniProtKB: Major capsid protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
300.0 mMKClPotassium Chloride
20.0 mMC3H4N2Imidazole
5.0 mMC2H6OSBeta-mercaptoethanol
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
Details: Grids were glow discharged at 25 mA for 60 sec with negative polarity.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.4312 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 40.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -44 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 395357
Segment selectionNumber selected: 619907
Startup modelType of model: NONE / Details: Ab initio map generated in cryoSPARC
Final angle assignmentType: NOT APPLICABLE

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