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- EMDB-14800: Tail tip of siphophage T5 : bent fibre after interaction with its... -

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Basic information

Entry
Database: EMDB / ID: EMD-14800
TitleTail tip of siphophage T5 : bent fibre after interaction with its bacterial receptor FhuA
Map data
Sample
  • Virus: Escherichia virus T5
    • Protein or peptide: Probable baseplate hub protein
    • Protein or peptide: Probable central straight fiber
KeywordsBacteriophage / Siphophage / T5 / baseplate / VIRAL PROTEIN
Function / homologyvirus tail, baseplate / virus tail / Baseplate hub protein pb3 / Straight fiber protein pb4
Function and homology information
Biological speciesEscherichia phage T5 (virus) / Escherichia virus T5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.32 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
DepositionApr 20, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14800.png

Downloads & links

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Map

FileDownload / File: emd_14800.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.351 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0346
Minimum - Maximum-0.043755263 - 0.12035153
Average (Standard dev.)0.00050336967 (±0.0042059673)
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_14800_msk_1.map
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Additional map: unsharpened map

Fileemd_14800_additional_1.map
Annotationunsharpened map
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Half map: #1

Fileemd_14800_half_map_1.map
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Half map: #2

Fileemd_14800_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: Probable baseplate hub protein
    • Protein or peptide: Probable central straight fiber

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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 with E. coli receptor FhuA reconstituted into nanodisc
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: Probable baseplate hub protein

MacromoleculeName: Probable baseplate hub protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 107.279766 KDa
SequenceString: MKKILDSAKN YLNTHDKLKT ACLIALELPS SSGSAATYIY LTDYFRDVTY NGILYRSGKV KSISSHKQNR QLSIGSLSFT ITGTAEDEV LKLVQNGVSF LDRGITIHQA IINEEGNILP VDPDTDGPLL FFRGRITGGG IKDNVNTSGI GTSVITWNCS N QFYDFDRV ...String:
MKKILDSAKN YLNTHDKLKT ACLIALELPS SSGSAATYIY LTDYFRDVTY NGILYRSGKV KSISSHKQNR QLSIGSLSFT ITGTAEDEV LKLVQNGVSF LDRGITIHQA IINEEGNILP VDPDTDGPLL FFRGRITGGG IKDNVNTSGI GTSVITWNCS N QFYDFDRV NGRYTDDASH RGLEVVNGTL QPSNGAKRPE YQEDYGFFHS NKSTTILAKY QVKEERYKLQ SKKKLFGLSR SY SLKKYYE TVTKEVDLDF NLAAKFIPVV YGVQKIPGIP IFADTELNNP NIVYVVYAFA EGEIDGFLDF YIGDSPMICF DET DSDTRT CFGRKKIVGD TMHRLAAGTS TSQPSVHGQE YKYNDGNGDI RIWTFHGKPD QTAAQVLVDI AKKKGFYLQN QNGN GPEYW DSRYKLLDTA YAIVRFTINE NRTEIPEISA EVQGKKVKVY NSDGTIKADK TSLNGIWQLM DYLTSDRYGA DITLD QFPL QKVISEAKIL DIIDESYQTS WQPYWRYVGW NDPLSENRQI VQLNTILDTS ESVFKNVQGI LESFGGAINN LSGEYR ITV EKYSTNPLRI NFLDTYGDLD LSDTTGRNKF NSVQASLVDP ALSWKTNSIT FYNSKFKEQD KGLDKKLQLS FANITNY YT ARSYADRELK KSRYSRTLSF SVPYKFIGIE PNDPIAFTYE RYGWKDKFFL VDEVENTRDG KINLVLQEYG EDVFINSE Q VDNSGNDIPD ISNNVLPPRD FKYTPTPGGV VGAIGKNGEL SWLPSLTNNV VYYSIAHSGH VNPYIVQQLE NNPNERMIQ EIIGEPAGLA IFELRAVDIN GRRSSPVTLS VDLNSAKNLS VVSNFRVVNT ASGDVTEFVG PDVKLAWDKI PEEEIIPEIY YTLEIYDSQ DRMLRSVRIE DVYTYDYLLT YNKADFALLN SGALGINRKL RFRIRAEGEN GEQSVGWATI

UniProtKB: Baseplate hub protein pb3

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Macromolecule #2: Probable central straight fiber

MacromoleculeName: Probable central straight fiber / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 74.851703 KDa
SequenceString: MISNNAPAKM VLNSVLTGYT LAYIQHSIYS DYDVIGRSFW LKEGSNVTRR DFTGIDTFSV TINNLKPTTT YEVQGAFYDS IIDSELLNA QIGINLSDKQ TFKMKSAPRI TGARCESEPV DVGVGAPIVY IDTTGEADYC TIELKDNSNA NNPWVKYYVG A LMPTIMFG ...String:
MISNNAPAKM VLNSVLTGYT LAYIQHSIYS DYDVIGRSFW LKEGSNVTRR DFTGIDTFSV TINNLKPTTT YEVQGAFYDS IIDSELLNA QIGINLSDKQ TFKMKSAPRI TGARCESEPV DVGVGAPIVY IDTTGEADYC TIELKDNSNA NNPWVKYYVG A LMPTIMFG GVPIGSYKVR ISGQISLPDG VTIDSSGYYE YPNVFEVRYN FVPPAAPINI VFKAARIADG KERYDLRVQW DW NRGAGAN VREFVLSYID SAEFVRTGWT KAQKINVGAA QSATIISFPW KVEHKFKVSS IAWGPDAQDV TDSAVQTFIL NES TPLDNS FVNETGIEVN YAYIKGKIKD GSTWKQTFLI DAATGAINIG LLDAEGKAPI SFDPVKKIVN VDGSVITKTI NAAN FVMTN LTGQDNPAIY TQGKTWGDTK SGIWMGMDNV TAKPKLDIGN ATQYIRYDGN ILRISSEVVI GTPNGDIDIQ TGIQG KQTV FIYIIGTSLP AKPTSPAYPP SGWSKTPPNR TSNTQNIYCS TGTLDPVTNQ LVSGTSWSDV VQWSGTEGVD GRPGAT GQR GPGMYSLAIA NLTAWNDSQA NSFFTSNFGS GPVKYDVLTE YKSGAPGTAF TRQWNGSAWT SPAMVLHGDM IVNGTVT AS KIVANNAFLS QIGVNIIYDR AAALSSNPEG SYKMKIDLQN GYIHIR

UniProtKB: Straight fiber protein pb4

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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 with E. coli receptor FhuA reconstituted into nanodisc

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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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0/3.1) / Number images used: 20349
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

RefinementProtocol: BACKBONE TRACE
Output model

PDB-7zn4:
Tail tip of siphophage T5 : bent fibre after interaction with its bacterial receptor FhuA

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