[English] 日本語
Yorodumi- EMDB-6271: Atomic structures of a bactericidal contractile nanotube in its p... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6271 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Atomic structures of a bactericidal contractile nanotube in its pre- and post-contraction states | |||||||||
Map data | Pyocin, contracted sheath | |||||||||
Sample |
| |||||||||
Keywords | pyocin / bacteriocin / sheath / tube | |||||||||
Function / homology | 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 / identical protein binding / Similar to FI genes of P2, phiCTX, and PS17: tail sheath Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Ge P / Scholl D / Leiman PG / Yu X / Miller JF / Zhou ZH | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2015 Title: Atomic structures of a bactericidal contractile nanotube in its pre- and postcontraction states. Authors: Peng Ge / Dean Scholl / Petr G Leiman / Xuekui Yu / Jeff F Miller / Z Hong Zhou / Abstract: R-type pyocins are representatives of contractile ejection systems, a class of biological nanomachines that includes, among others, the bacterial type VI secretion system (T6SS) and contractile ...R-type pyocins are representatives of contractile ejection systems, a class of biological nanomachines that includes, among others, the bacterial type VI secretion system (T6SS) and contractile bacteriophage tails. We report atomic models of the Pseudomonas aeruginosa precontraction pyocin sheath and tube, and the postcontraction sheath, obtained by cryo-EM at 3.5-Å and 3.9-Å resolutions, respectively. The central channel of the tube is negatively charged, in contrast to the neutral and positive counterparts in T6SSs and phage tails. The sheath is interwoven by long N- and C-terminal extension arms emanating from each subunit, which create an extensive two-dimensional mesh that has the same connectivity in the extended and contracted state of the sheath. We propose that the contraction process draws energy from electrostatic and shape complementarities to insert the inner tube through bacterial cell membranes to eventually kill the bacteria. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6271.map.gz | 36.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6271-v30.xml emd-6271.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | 400_6271.gif 80_6271.gif | 112 KB 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6271 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6271 | HTTPS FTP |
-Validation report
Summary document | emd_6271_validation.pdf.gz | 424.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6271_full_validation.pdf.gz | 424.3 KB | Display | |
Data in XML | emd_6271_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6271 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6271 | HTTPS FTP |
-Related structure data
Related structure data | 3j9rMC 6270C 3j9qC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6271.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Pyocin, contracted sheath | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.104 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Pyocin (post-contraction)
Entire | Name: Pyocin (post-contraction) |
---|---|
Components |
|
-Supramolecule #1000: Pyocin (post-contraction)
Supramolecule | Name: Pyocin (post-contraction) / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 1 |
---|
-Macromolecule #1: pyocin tail sheath
Macromolecule | Name: pyocin tail sheath / type: protein_or_peptide / ID: 1 / Name.synonym: sheath / Oligomeric state: helix of hexameric rings / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO |
Sequence | UniProtKB: Similar to FI genes of P2, phiCTX, and PS17: tail sheath |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.4 / Details: 1x PBS |
---|---|
Grid | Details: baked 1.2/1.3 Quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: blot time 4 seconds, blot force 1 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Average: 80 K |
Details | Scanned with 9200 ED |
Date | Oct 7, 2009 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 307 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Relion-based IHRSR |
---|---|
Final reconstruction | Applied symmetry - Helical parameters - Δz: 16.2 Å Applied symmetry - Helical parameters - Δ&Phi: 33.1 ° Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: OTHER / Software - Name: Relion, IHRSR |
CTF correction | Details: Each particle |