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- PDB-8bcu: Cryo-EM structure of the proximal end of bacteriophage T5 tail, a... -

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Basic information

Entry
Database: PDB / ID: 8bcu
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
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
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 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: 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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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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
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area34370 Å2
ΔGint-108 kcal/mol
Surface area92910 Å2
MethodPISA

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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

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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, incubated with the bacterial receptor FhuA reconstituted in nanodiscs
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 chlorideNaClSodium chloride1
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, incubated with the bacterial receptor FhuA reconstituted in nanodiscs
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 + 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)

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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 FIELDBright-field microscopy / 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: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10701 / Symmetry type: POINT
Atomic model buildingB value: 120 / Protocol: BACKBONE TRACE / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418609
ELECTRON MICROSCOPYf_angle_d0.5125302
ELECTRON MICROSCOPYf_dihedral_angle_d4.1462529
ELECTRON MICROSCOPYf_chiral_restr0.0422934
ELECTRON MICROSCOPYf_plane_restr0.0033282

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