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- EMDB-15968: Cryo-EM structure of the proximal end of bacteriophage T5 tail, a... -

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Basic information

Entry
Database: EMDB / ID: EMD-15968
TitleCryo-EM structure of the proximal end of bacteriophage T5 tail, after interaction with its receptor : 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
Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / 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) / Escherichia virus T5
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 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: To Be Published
Title: Cryo-EM structure of the proximal end of bacteriophage T5 tail, in its native state and after interaction with its bacterial receptor
Authors: Linares R / Effantin G / Breyton C
History
DepositionOct 17, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15968.png

Downloads & links

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Map

FileDownload / File: emd_15968.map.gz / Format: CCP4 / Size: 10.5 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 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

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: 0.043
Minimum - Maximum-0.08694504 - 0.16651808
Average (Standard dev.)0.0017578213 (±0.009861981)
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_15968_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Additional map: #1

Fileemd_15968_additional_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_15968_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15968_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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: 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, incubated with the bacterial receptor FhuA reconstituted in nanodiscs
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 chloridesodium 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 + FhuA-nanodisc 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 ...Details: 3 uL of T5 tails + FhuA-nanodisc 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, incubated with the bacterial receptor FhuA reconstituted in nanodiscs

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
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
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)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0/3.1) / Number images used: 10701
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 120
Output model

PDB-8bcu:
Cryo-EM structure of the proximal end of bacteriophage T5 tail, after interaction with its receptor : p142 tail terminator protein hexamer and pb6 tail tube protein trimer

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