+Open data
-Basic information
Entry | Database: PDB / ID: 6pyt | |||||||||||||||
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Title | CryoEM Structure of Pyocin R2 - precontracted - trunk | |||||||||||||||
Components |
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Keywords | ANTIMICROBIAL PROTEIN / bacteriocin / pyocin / helix | |||||||||||||||
Function / homology | Tail tube protein / Phage tail tube protein FII / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Probable bacteriophage protein / Probable bacteriophage protein Function and homology information | |||||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
Authors | Ge, P. / Avaylon, J. / Scholl, D. / Shneider, M.M. / Browning, C. / Buth, S.A. / Plattner, M. / Ding, K. / Leiman, P.G. / Miller, J.F. / Zhou, Z.H. | |||||||||||||||
Funding support | United States, Switzerland, 4items
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Citation | Journal: Nature / Year: 2020 Title: Action of a minimal contractile bactericidal nanomachine. Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff ...Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff F Miller / Z Hong Zhou / Abstract: R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded ...R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold. Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage. Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes; the dissociation then initiates a cascade of events leading to sheath contraction; and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pyt.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6pyt.ent.gz | 886.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/6pyt ftp://data.pdbj.org/pub/pdb/validation_reports/py/6pyt | HTTPS FTP |
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-Related structure data
Related structure data | 20526MC 5cesC 6u5bC 6u5fC 6u5hC 6u5jC 6u5kC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 17957.352 Da / Num. of mol.: 12 / Source method: isolated from a natural source Source: (natural) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: Q9I5S9 #2: Protein | Mass: 41247.332 Da / Num. of mol.: 12 / Source method: isolated from a natural source Source: (natural) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 References: UniProt: G3XD39 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Pyocin R2 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Details: Baked, glow discharged for 4 min before use / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2160 nm / Nominal defocus min: 2160 nm / Calibrated defocus min: 1100 nm / Calibrated defocus max: 3400 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 81 K / Temperature (min): 80 K |
Image recording | Average exposure time: 10 sec. / Electron dose: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7331 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter upper: 10 eV / Energyfilter lower: -10 eV |
Image scans | Movie frames/image: 50 / Used frames/image: 3-13 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 18.3 ° / Axial rise/subunit: 39.46 Å / Axial symmetry: C6 | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 15684 | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15487 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |