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- EMDB-13953: Tail tip of siphophage T5 : common core proteins -

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Basic information

Entry
Database: EMDB / ID: EMD-13953
TitleTail tip of siphophage T5 : common core proteins
Map data
Sample
  • Virus: Escherichia virus T5
    • Protein or peptide: L-shaped tail fiber protein p132
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Distal tail protein
    • Protein or peptide: Tail tube protein
KeywordsBacteriophage / Siphophage / T5 / baseplate / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / virus tail, fiber / virus tail / viral release from host cell by cytolysis
Similarity search - Function
: / : / : / Distal tail protein pb9, A domain C-terminal / Distal tail protein pb9, A domain, N-terminal / Distal tail protein pb9, B domain / 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 protein pb6 / Baseplate tube protein p140 / Distal tail protein pb9 / Collar protein p132
Similarity search - Component
Biological speciesEscherichia phage T5 (virus) / Escherichia virus T5
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsLinares R / Arnaud CA / Effantin G / Darnault C / Epalle N / Boeri Erba E / Schoehn G / Breyton C
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: Sci Adv / Year: 2023
Title: Structural basis of bacteriophage T5 infection trigger and cell wall perforation.
Authors: Romain Linares / Charles-Adrien Arnaud / Grégory Effantin / Claudine Darnault / Nathan Hugo Epalle / Elisabetta Boeri Erba / Guy Schoehn / Cécile Breyton /
Abstract: Most bacteriophages present a tail allowing host recognition, cell wall perforation, and viral DNA channeling from the capsid to the infected bacterium cytoplasm. The majority of tailed phages bear a ...Most bacteriophages present a tail allowing host recognition, cell wall perforation, and viral DNA channeling from the capsid to the infected bacterium cytoplasm. The majority of tailed phages bear a long flexible tail () at the tip of which receptor binding proteins (RBPs) specifically interact with their host, triggering infection. In siphophage T5, the unique RBP is located at the extremity of a central fiber. We present the structures of T5 tail tip, determined by cryo-electron microscopy before and after interaction with its receptor, FhuA, reconstituted into nanodisc. These structures bring out the important conformational changes undergone by T5 tail tip upon infection, which include bending of T5 central fiber on the side of the tail tip, tail anchoring to the membrane, tail tube opening, and formation of a transmembrane channel. The data allow to detail the first steps of an otherwise undescribed infection mechanism.
History
DepositionDec 7, 2021-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13953.png

Downloads & links

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Map

FileDownload / File: emd_13953.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 240 pix.
= 324.24 Å		1.35 Å/pix.
x 240 pix.
= 324.24 Å		1.35 Å/pix.
x 240 pix.
= 324.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.351 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0471
Minimum - Maximum-0.13373959 - 0.2244534
Average (Standard dev.)0.000740347 (±0.0087395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 324.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13953_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13953_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13953_half_map_2.map
Projections & Slices
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Histogram (log scale)

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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: L-shaped tail fiber protein p132
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Distal tail protein
    • 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, incubated or not with the bacterial receptor FhuA
NCBI-ID: 2695836 / Sci species name: Escherichia virus T5 / 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: L-shaped tail fiber protein p132

MacromoleculeName: L-shaped tail fiber protein p132 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 15.079864 KDa
SequenceString:
MSTENRVIDL VVDENVPYGL LMQFMDVDDS VYPSTSKPVD LTDFSLRGSI KSSLEDGAET VASFTTAIVD AAQGVASISL PVSAVTTIA SKASKERDRY NPRQRLAGYY DVIITRTAVG SAASSFRIME GKVYISDGVT Q

UniProtKB: Collar protein p132

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Macromolecule #2: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 34.367605 KDa
SequenceString: MFYSLMRESK IVIEYDGRGY HFDALSNYDA STSFQEFKTL RRTIHNRTNY ADSIINAQDP SSISLAINFS TTLIESNFFD WMGFTREGN SLFLPRNTPN IEPIMFNMYI INHNNSCIYF ENCYVSTVDF SLDKSIPILN VGIESGKFSE VSTFRDGYTI T QGEVLPYS ...String:
MFYSLMRESK IVIEYDGRGY HFDALSNYDA STSFQEFKTL RRTIHNRTNY ADSIINAQDP SSISLAINFS TTLIESNFFD WMGFTREGN SLFLPRNTPN IEPIMFNMYI INHNNSCIYF ENCYVSTVDF SLDKSIPILN VGIESGKFSE VSTFRDGYTI T QGEVLPYS APAVYTNSSP LPALISASMS FQQQCSWRED RNIFDINKIY TNKRAYVNEM NASATLAFYY VKRLVGDKFL NL DPETRTP LIIKNKYVSI TFPLARISKR LNFSDLYQVE YDVIPTADSD PVEINFFGER K

UniProtKB: Baseplate tube protein p140

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Macromolecule #3: Distal tail protein

MacromoleculeName: Distal tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 22.798641 KDa
SequenceString: MRLPDPYTNP EYPGLGFESV NLVDNDPMIR DELPNGKVKE VKISAQYWGI NISYPELFPD EYAFLDSRLL EYKRTGDYLD VLLPQYEAF RVRGDTKSVT IPAGQKGSQI ILNTNGTLTG QPKAGDLFKL STHPKVYKIT NFSSSGNVWN ISLYPDLFIT T TGSEKPVF ...String:
MRLPDPYTNP EYPGLGFESV NLVDNDPMIR DELPNGKVKE VKISAQYWGI NISYPELFPD EYAFLDSRLL EYKRTGDYLD VLLPQYEAF RVRGDTKSVT IPAGQKGSQI ILNTNGTLTG QPKAGDLFKL STHPKVYKIT NFSSSGNVWN ISLYPDLFIT T TGSEKPVF NGILFRTKLM NGDSFGSTLN NNGTYSGISL SLRESL

UniProtKB: Distal tail protein pb9

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Macromolecule #4: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / 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: intensity 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 (with or without FhuA-ND) were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot ...Details: 3 uL of T5 tails sample (with or without FhuA-ND) 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, incubated or not with the bacterial receptor FhuA

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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: low-resolution reconstruction from a previous data collection
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0/3.1) / Number images used: 29639
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

DetailsAtomic protein models were built into the different cryo-EM maps using the Coot software by tracing the protein sequence into the densities and were then iteratively refined alternating Coot manual refinement and PHENIX real space refine tool until convergence. p140, p132, BHPpb3 and TMPpb2 C-ter models were built ab initio. For TTPpb6 and DTPpb9 models, already existing X-ray models (PDB codes 5NGJ / 4JMQ) were used as a starting point and were refined into the EM maps. Molprobity was used for model quality assessment.
RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 112
Output model

PDB-7qg9:
Tail tip of siphophage T5 : common core proteins

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