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- PDB-7zn4: Tail tip of siphophage T5 : bent fibre after interaction with its... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zn4 | |||||||||
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Title | Tail tip of siphophage T5 : bent fibre after interaction with its bacterial receptor FhuA | |||||||||
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![]() | VIRAL PROTEIN / Bacteriophage / Siphophage / T5 / baseplate | |||||||||
Function / homology | virus tail, baseplate / virus tail / Baseplate hub protein pb3 / Straight fiber protein pb4![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.32 Å | |||||||||
![]() | Linares, R. / Arnaud, C.A. / Effantin, G. / Darnault, C. / Epalle, N. / Boeri Erba, E. / Schoehn, G. / Breyton, C. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 473.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 14800MC ![]() 7qg9C ![]() 7zhjC ![]() 7zlvC ![]() 7zn2C ![]() 7zqbC ![]() 7zqpC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 107279.766 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 74851.703 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Escherichia virus T5 / Type: VIRUS 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 Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE | |||||||||||||||||||||||||
Natural host | Organism: Escherichia coli / Strain: F | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding 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 E. coli receptor FhuA reconstituted into nanodisc | |||||||||||||||||||||||||
Specimen support | Details: Intensity 25 mA / Grid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20349 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE |