+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20646 | |||||||||||||||
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Title | CryoEM Structure of Pyocin R2 - precontracted - hub | |||||||||||||||
Map data | CryoEM Structure of Pyocin R2 - precontracted - hub | |||||||||||||||
Sample |
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Keywords | bacteriocin / pyocin / UNKNOWN FUNCTION | |||||||||||||||
Function / homology | : / virus tail / Uncharacterized protein Function and homology information | |||||||||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||||||||
Authors | Ge P / Avaylon J | |||||||||||||||
Funding support | United States, Switzerland, 4 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20646.map.gz | 116.4 MB | EMDB map data format | |
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Header (meta data) | emd-20646-v30.xml emd-20646.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_20646.png | 339.8 KB | ||
Filedesc metadata | emd-20646.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20646 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20646 | HTTPS FTP |
-Related structure data
Related structure data | 6u5hMC 5cesC 6pytC 6u5bC 6u5fC 6u5jC 6u5kC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20646.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM Structure of Pyocin R2 - precontracted - hub | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.041 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pyocin R2
Entire | Name: Pyocin R2 |
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Components |
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-Supramolecule #1: Pyocin R2
Supramolecule | Name: Pyocin R2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
-Macromolecule #1: Probable bacteriophage protein Pyocin R2
Macromolecule | Name: Probable bacteriophage protein Pyocin R2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: 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 |
Molecular weight | Theoretical: 35.919727 KDa |
Sequence | String: MQPSFRIVAD GTDVTQRLND RLLKLTLLDK PGMESDSLTL RIDDRDGQVA LPRRGAVLEV HLGYAGEPLM RMGRFTVDTL QWAGPPDCL TVTAKAGDMR GSGKTIRSGG WEGTTLAQVC RDVGARNGWR VECPLQVAIA RVDQVNESDY HFVTRLARQY D CTAKLAEG ...String: MQPSFRIVAD GTDVTQRLND RLLKLTLLDK PGMESDSLTL RIDDRDGQVA LPRRGAVLEV HLGYAGEPLM RMGRFTVDTL QWAGPPDCL TVTAKAGDMR GSGKTIRSGG WEGTTLAQVC RDVGARNGWR VECPLQVAIA RVDQVNESDY HFVTRLARQY D CTAKLAEG MLMVLPRQSG QSATGRRIEP LVLGRADVGS FDVTFDDRSL MRTVKTRYQL PGSGEVKSVE LKNPKAPATA MG EHVDRHL YTSRGEAEQA AKARLASFSR SSASVRLELP GRGDLFAERS LLLQGFKAGI DGEFLIDSVE HTYSSSGWTT VVQ CNGGRG GKG UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Details: unspecified | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.4 µm / Calibrated defocus min: 1.1 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.16 µm / Nominal defocus min: 2.16 µm / Nominal magnification: 130000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 80.0 K / Max: 81.0 K |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-20 / Number grids imaged: 1 / Number real images: 7331 / Average exposure time: 10.0 sec. / Average electron dose: 80.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 43939 |
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Startup model | Type of model: NONE |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4) |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: RELION (ver. 1.4) / Details: Map-Model FSC 0.5 / Number images used: 18290 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6u5h: |