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- EMDB-15967: Cryo-EM structure of the proximal end of bacteriophage T5 tail : ... -

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Basic information

Entry
Database: EMDB / ID: EMD-15967
TitleCryo-EM structure of the proximal end of bacteriophage T5 tail : p142 tail terminator protein hexamer and pb6 tail tube protein trimer
Map data
Sample
  • Virus: Escherichia virus T5
    • Protein or peptide: Tail tube terminator protein p142
    • Protein or peptide: Tail tube protein
KeywordsBacteriophage / Siphophage / T5 / tail terminator / Trp / VIRAL PROTEIN
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
: / Bacteriophage Tail Tube Terminator Protein / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Invasin/intimin cell-adhesion fragments / 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) / Escherichia virus T5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsLinares R / Effantin G / Breyton C / Darnault C / Epalle N / Boeri Erba E / Schoehn G
Funding support France, 2 items
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, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15967.png

Downloads & links

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Map

FileDownload / File: emd_15967.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 140 pix.
= 189.14 Å		1.35 Å/pix.
x 140 pix.
= 189.14 Å		1.35 Å/pix.
x 140 pix.
= 189.14 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.351 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.20446527 - 0.27868882
Average (Standard dev.)0.0015227989 (±0.0136231305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 189.14 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15967_msk_1.map
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Additional map: unsharpened map

Fileemd_15967_additional_1.map
Annotationunsharpened map
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Half map: #2

Fileemd_15967_half_map_1.map
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Half map: #1

Fileemd_15967_half_map_2.map
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Sample components

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Entire : Escherichia virus T5

EntireName: Escherichia virus T5
Components
  • Virus: Escherichia virus T5
    • Protein or peptide: Tail tube terminator protein p142
    • Protein or peptide: Tail tube protein

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Supramolecule #1: Escherichia virus T5

SupramoleculeName: Escherichia virus T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d
NCBI-ID: 2695836 / Sci species name: Escherichia virus T5 / Sci species strain: T5D20am30d / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / Strain: F

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Macromolecule #1: Tail tube terminator protein p142

MacromoleculeName: Tail tube terminator protein p142 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 18.378643 KDa
SequenceString:
MDHRTSIAQA MVDRISKQMD GSQPDEYFNN LYGNVSRQTY KFEEIREFPY VAVHIGTETG QYLPSGQQWM FLELPILVYD KEKTDIQEQ LEKLVADIKT VIDTGGNLEY TVSKPNGSTF PCEATDMIIT SVSTDEGLLA PYGLAEINVT VRYQPPRRSL R R

UniProtKB: Tail tube terminator protein p142

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Macromolecule #2: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 50.459215 KDa
SequenceString: MSLQLLRNTR IFVSTVKTGH NKTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAEW SFSTYILPYK DKNTSKQIV PDYMLWHALS SGRAINLEGT TGAHNNATNF MVNFKDNSYH ELAMLHIYIL TDKTWSYIDS CQINQAEVNV D IEDIGRVT ...String:
MSLQLLRNTR IFVSTVKTGH NKTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAEW SFSTYILPYK DKNTSKQIV PDYMLWHALS SGRAINLEGT TGAHNNATNF MVNFKDNSYH ELAMLHIYIL TDKTWSYIDS CQINQAEVNV D IEDIGRVT WSGNGNQLIP LDEQPFDPDQ IGIDDETYMT IQGSYIKNKL TILKIKDMDT NKSYDIPITG GTFTINNNIT YL TPNVMSR VTIPIGSFTG AFELTGSLTA YLNDKSLGSM ELYKDLIKTL KVVNRFEIAL VLGGEYDDER PAAILVAKQA HVN IPTIET DDVLGTSVEF KAIPSDLDAG DEGYLGFSSK YTRTTINNLI VNGDGATDAV TAITVKSAGN VTTLNRSATL QMSV EVTPS SARNKEVTWA ITAGDAATIN ATGLLRADAS KTGAVTVEAT AKDGSGVKGT KVITVTAGG

UniProtKB: Tail tube protein pb6

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
100.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride
1.0 mMCaCl2calcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV
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).
DetailsPure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: A 9-nm diameter cylinder was generated using relion_image_handler and used as an initial model for 3D classification. A relevant 3D class map was then used as initial model for 3D refinement
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0/3.1) / Number images used: 9952
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0/3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0/3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 146
Output model

PDB-8bcp:
Cryo-EM structure of the proximal end of bacteriophage T5 tail : p142 tail terminator protein hexamer and pb6 tail tube protein trimer

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