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- PDB-8bcp: Cryo-EM structure of the proximal end of bacteriophage T5 tail : ... -

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Basic information

Entry
Database: PDB / ID: 8bcp
TitleCryo-EM structure of the proximal end of bacteriophage T5 tail : p142 tail terminator protein hexamer and pb6 tail tube protein trimer
Components
  • Tail tube protein
  • Tail tube terminator protein p142
KeywordsVIRAL PROTEIN / Bacteriophage / Siphophage / T5 / tail terminator / Trp
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / viral release from host cell by cytolysis
Similarity search - Function
Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Tail tube terminator protein p142 / Tail tube protein pb6
Similarity search - Component
Biological speciesEscherichia phage T5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsLinares, R. / Effantin, G. / Breyton, C.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0027 France
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0023 France
CitationJournal: J Virol / Year: 2025
Title: About bacteriophage tail terminator and tail completion proteins: structure of the proximal extremity of siphophage T5 tail.
Authors: Romain Linares / Cécile Breyton /
Abstract: Bacteriophages are viruses infecting bacteria. The vast majority of them bear a tail, allowing host recognition, cell wall perforation, and DNA injection into the host cytoplasm. Using electron cryo- ...Bacteriophages are viruses infecting bacteria. The vast majority of them bear a tail, allowing host recognition, cell wall perforation, and DNA injection into the host cytoplasm. Using electron cryo-microscopy (cryo-EM) and single particle analysis, we determined the organization of the tail proximal extremity of siphophage T5 that possesses a long flexible tail and solved the structure of its tail terminator protein p142 (TrP). It allowed us to confirm the common evolutionary origin between T5 TrP and other known or putative TrPs from siphophages, myophages, and bacterial tail-like machines, despite very poor sequence conservation. By also determining the structure of the T5 tail proximal extremity after interaction with T5 bacterial receptor FhuA, we showed that no conformational changes occur in TrP and confirmed that the infection signal transduction is not carried by the tube itself. We also investigated the location of T5 Neck1 or tail completion protein p143 (TCP) and showed, thanks to a combination of cryo-EM and structure prediction using Alphafold2, that it is not located at the capsid-to-tail interface as suggested by its position in the genome, but instead, very unexpectedly, on the side of T5 tail tip, and that it appears to be monomeric. Based on structure comparison with other putative TCPs predicted structures, this feature could not be shared by other TCPs and questions the affiliation of p143 to this family of protein.IMPORTANCEBacteriophages, viruses infecting bacteria, are the most abundant living entities on Earth. They are present in all ecosystems where bacteria develop and are instrumental in the regulation, diversity, evolution, and pathogeny of microbial populations. Moreover, with the increasing number of pathogenic strains resistant to antibiotics, virulent phages are considered a serious alternative or complement to classical treatments. 96% of all phages present a tail that allows host recognition and safe channeling of the DNA to the host cytoplasm. We present the atomic model of the proximal extremity of the siphophage T5 tail, confirming structural similarities with other phages. This structure, combined with results previously published and further explored, also allowed a review and a discussion on the role and localization of a mysterious tail protein, the tail completion protein, which is known to be present in the phage tails, but that was never identified in a phage structure.
History
DepositionOct 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Tail tube terminator protein p142
D: Tail tube terminator protein p142
H: Tail tube protein
A: Tail tube terminator protein p142
B: Tail tube terminator protein p142
G: Tail tube protein
E: Tail tube terminator protein p142
F: Tail tube terminator protein p142
I: Tail tube protein


Theoretical massNumber of molelcules
Total (without water)261,6509
Polymers261,6509
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33460 Å2
ΔGint-100 kcal/mol
Surface area95270 Å2

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Components

#1: Protein
Tail tube terminator protein p142 / TrP-142 / Tail protein p142 / Tail-to-head joining protein p142 / THJP


Mass: 18378.643 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGE1
#2: Protein Tail tube protein / TTP / Tail protein pb6


Mass: 50459.215 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGE2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Escherichia virus T5 / Type: VIRUS
Details: Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia virus T5 / Strain: T5D20am30d
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Escherichia coli / Strain: F
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTrisC4H11NO31
2100 mMsodium chlorideNaCl1
31 mMmagnesium chlorideMgCl21
41 mMcalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d
Specimen supportDetails: 25 mA / Grid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K
Details: 3 uL of T5 tails sample were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100 percent ...Details: 3 uL of T5 tails sample were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100 percent humidity, 20 Celsius degrees, 5 s blotting time, blot force 0)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
9RELION3.0/3.1initial Euler assignment
10RELION3.0/3.1final Euler assignment
12RELION3.0/3.13D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9952 / Symmetry type: POINT
Atomic model buildingB value: 146 / Protocol: BACKBONE TRACE / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318501
ELECTRON MICROSCOPYf_angle_d0.50225161
ELECTRON MICROSCOPYf_dihedral_angle_d3.9442511
ELECTRON MICROSCOPYf_chiral_restr0.0432919
ELECTRON MICROSCOPYf_plane_restr0.0043264

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