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Yorodumi- PDB-7xtg: Cryo-EM structure of Listeria monocytogenes man-PTS complexed wit... -
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-Basic information
Entry | Database: PDB / ID: 7xtg | |||||||||
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Title | Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1 | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Bacteriocin / PTS / ManYZ / ManY / ManZ / transporter / Mannose / PROTEIN TRANSPORT / Listeria monocytogenes / Pediococcus acidilactici / Latilactobacillus sakei / Mannose Phosphotransferase System / Man-PTS | |||||||||
Function / homology | Function and homology information bacteriocin immunity / phosphoenolpyruvate-dependent sugar phosphotransferase system / transferase activity / killing of cells of another organism / defense response to bacterium / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Pediococcus acidilactici (bacteria) Latilactobacillus sakei (bacteria) Listeria monocytogenes (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Zeng, J.W. / Wang, J.W. / Zhu, L.Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Appl Environ Microbiol / Year: 2022 Title: Structural Basis of the Immunity Mechanisms of Pediocin-like Bacteriocins. Authors: Liyan Zhu / Jianwei Zeng / Jiawei Wang / Abstract: Pediocin-like bacteriocins, also designated class IIa bacteriocins, are ribosomally synthesized antimicrobial peptides targeting species closely related to the producers. They act on the cytoplasmic ...Pediocin-like bacteriocins, also designated class IIa bacteriocins, are ribosomally synthesized antimicrobial peptides targeting species closely related to the producers. They act on the cytoplasmic membrane of Gram-positive cells by dissipating the transmembrane electrical potential through pore formation with the mannose phosphotransferase system (man-PTS) as the target/receptor. Bacteriocin-producing strains also synthesize a cognate immunity protein that protects them against their own bacteriocins. Herein, we report the cryo-electron microscopy structure of the bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei. The complex structure reveals that pediocin-like bacteriocins bind to the same position on the Core domain of man-PTS, while the C-terminal helical tails of bacteriocins delimit the opening range of the Core domain away from the Vmotif domain to facilitate transmembrane pore formation. Upon attack of bacteriocins from the extracellular side, man-PTS exposes its cytosolic side for recognition of the N-terminal four-helix bundle of the immunity protein. The C-terminal loop of the immunity protein then inserts into the pore and blocks leakage induced by bacteriocins. Elucidation of the toxicity and immunity mechanisms of pediocin-like bacteriocins could support the design of novel bacteriocins against antibiotic-resistant pathogenic bacteria. Pediocin-like bacteriocins, ribosomally synthesized antimicrobial peptides, are generally co-expressed with cognate immunity proteins to protect the bacteriocin-producing strain from its own bacteriocin. Bacteriocins are considered potential alternatives to conventional antibiotics in the context of the bacterial resistance crisis, but the immunity mechanism is unclear. This study uncovered the mechanisms of action and immunity of class IIa bacteriocins. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xtg.cif.gz | 337.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xtg.ent.gz | 278.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xtg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/7xtg ftp://data.pdbj.org/pub/pdb/validation_reports/xt/7xtg | HTTPS FTP |
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-Related structure data
Related structure data | 33448MC 7xnoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein/peptide | Mass: 4444.088 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pediococcus acidilactici (bacteria) / Gene: curA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A311 #2: Protein | Mass: 10213.867 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Latilactobacillus sakei (bacteria) / Gene: saiA / Production host: Escherichia coli (E. coli) / References: UniProt: Q48864 #3: Protein | Mass: 25461.646 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) Gene: manY, levF, CW750_06585, GJ664_06230, LAS9624_02106, LSAJ64_0482 Production host: Escherichia coli (E. coli) / References: UniProt: A0A094YUG1 #4: Protein | Mass: 33000.723 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) Gene: levG, manZ, CW750_06590, GJ664_06235, LAS9624_02107, LSAJ64_0483 Production host: Escherichia coli (E. coli) / References: UniProt: A0A094XZA1 #5: Sugar | Has ligand of interest | Y | |
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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 |
-Sample preparation
Component | Name: Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1 and sakacin-A immunity factor Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Listeria monocytogenes (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178777 / Symmetry type: POINT |