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

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Basic information

Entry
Database: PDB / ID: 7qg9
TitleTail tip of siphophage T5 : common core proteins
Components
  • Distal tail protein
  • L-shaped tail fiber protein p132
  • Minor tail protein
  • Tail tube protein
KeywordsVIRAL PROTEIN / Bacteriophage / Siphophage / T5 / baseplate
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsLinares, R. / Arnaud, C.A. / Effantin, G. / Darnault, C. / Epalle, N. / Boeri Erba, E. / Schoehn, 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: 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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Source and taxonomy / Category: em_entity_assembly_naturalsource / entity_src_nat
Item: _em_entity_assembly_naturalsource.ncbi_tax_id / _entity_src_nat.common_name ..._em_entity_assembly_naturalsource.ncbi_tax_id / _entity_src_nat.common_name / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific
Revision 1.2Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: L-shaped tail fiber protein p132
I: Minor tail protein
a: Distal tail protein
Q: L-shaped tail fiber protein p132
S: L-shaped tail fiber protein p132
F: Tail tube protein
N: L-shaped tail fiber protein p132
H: Minor tail protein
X: Distal tail protein
Y: Distal tail protein
M: L-shaped tail fiber protein p132
O: L-shaped tail fiber protein p132
E: Tail tube protein
C: Tail tube protein
J: L-shaped tail fiber protein p132
L: L-shaped tail fiber protein p132
G: Minor tail protein
W: Distal tail protein
U: L-shaped tail fiber protein p132
K: L-shaped tail fiber protein p132
D: Tail tube protein
A: Tail tube protein
B: Tail tube protein
P: L-shaped tail fiber protein p132
T: L-shaped tail fiber protein p132
V: Distal tail protein
Z: Distal tail protein


Theoretical massNumber of molelcules
Total (without water)723,60827
Polymers723,60827
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
L-shaped tail fiber protein p132


Mass: 15079.864 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q7Y5D9
#2: Protein Minor tail protein / Tail protein p140


Mass: 34367.605 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGE3
#3: Protein
Distal tail protein / Dit / Tail protein pb9


Mass: 22798.641 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage T5 (virus) / References: UniProt: Q6QGE8
#4: Protein
Tail tube protein / TTP / Tail protein pb6


Mass: 50459.215 Da / Num. of mol.: 6 / 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 or not with the bacterial receptor FhuA
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia virus T5
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 chlorideNaCl1
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 or not with the bacterial receptor FhuA
Specimen supportDetails: intensity 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 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)

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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 FIELD / 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

EM software
IDNameVersionCategoryDetails
1EMAN2particle selectionmanual particle picking was performed using EMAN2/e2helixboxer
2EPUimage acquisition
4GctfCTF correction
9RELION3.0/3.1initial Euler assignment
10RELION3.0/3.1final Euler assignment
12RELION3.0/3.13D reconstruction
19PHENIXmodel refinement
20Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29639 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 112 / Protocol: BACKBONE TRACE / Space: REAL
Details: Atomic 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 ...Details: Atomic 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.

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