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- EMDB-33448: Cryo-EM structure of Listeria monocytogenes man-PTS complexed wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-33448
TitleCryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1
Map data
Sample
  • Complex: Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1 and sakacin-A immunity factor
    • Protein or peptide: Bacteriocin curvacin-A
    • Protein or peptide: Sakacin-A immunity factor
    • Protein or peptide: Mannose permease IIC component
    • Protein or peptide: Mannose permease IID component
  • Ligand: alpha-D-mannopyranose
KeywordsBacteriocin / PTS / ManYZ / ManY / ManZ / transporter / Mannose / PROTEIN TRANSPORT / Membrane Protein / Listeria monocytogenes / Pediococcus acidilactici / Latilactobacillus sakei / Mannose Phosphotransferase System / Man-PTS
Function / homology
Function and homology information


bacteriocin immunity / phosphoenolpyruvate-dependent sugar phosphotransferase system / killing of cells of another organism / defense response to bacterium / extracellular region / membrane / plasma membrane
Similarity search - Function
Bacteriocin-type signal sequence / Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS system sorbose-specific iic component / PTS system mannose/fructose/sorbose family IID component / PTS_EIIC type-4 domain profile. / PTS_EIID domain profile. / : / Bacteriocin, class IIa / Bacteriocin, class IIa, conserved site ...Bacteriocin-type signal sequence / Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS system sorbose-specific iic component / PTS system mannose/fructose/sorbose family IID component / PTS_EIIC type-4 domain profile. / PTS_EIID domain profile. / : / Bacteriocin, class IIa / Bacteriocin, class IIa, conserved site / Bacteriocin class IIa domain superfamily / Class II bacteriocin / Bacteriocin class IIa family signature.
Similarity search - Domain/homology
Mannose permease IID component / Mannose permease IIC component / Bacteriocin curvacin-A / Sakacin-A immunity factor
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria) / Pediococcus acidilactici (bacteria) / Latilactobacillus sakei (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsZeng JW / Wang JW / Zhu LY
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501103 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: 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
DepositionMay 17, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33448.png

Downloads & links

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Map

FileDownload / File: emd_33448.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 269.856 Å		0.84 Å/pix.
x 320 pix.
= 269.856 Å		0.84 Å/pix.
x 320 pix.
= 269.856 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8433 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.5694256 - 3.182501
Average (Standard dev.)0.0019709964 (±0.08894118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 269.856 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33448_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33448_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Listeria monocytogenes man-PTS complexed wit...

EntireName: Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1 and sakacin-A immunity factor
Components
  • Complex: Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1 and sakacin-A immunity factor
    • Protein or peptide: Bacteriocin curvacin-A
    • Protein or peptide: Sakacin-A immunity factor
    • Protein or peptide: Mannose permease IIC component
    • Protein or peptide: Mannose permease IID component
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Cryo-EM structure of Listeria monocytogenes man-PTS complexed wit...

SupramoleculeName: Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1 and sakacin-A immunity factor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Listeria monocytogenes (bacteria)

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Macromolecule #1: Bacteriocin curvacin-A

MacromoleculeName: Bacteriocin curvacin-A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pediococcus acidilactici (bacteria)
Molecular weightTheoretical: 4.444088 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARSYGNGVY CNNKKCWVNR GEATQSIIGG MISGWASGLA GM

UniProtKB: Bacteriocin curvacin-A

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Macromolecule #2: Sakacin-A immunity factor

MacromoleculeName: Sakacin-A immunity factor / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Latilactobacillus sakei (bacteria)
Molecular weightTheoretical: 10.213867 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ADYKKINSIL TYTSTALKNP KIIKDKDLVV LLTIIQEEAK QNRIFYDYKR KFRPAVTRFT IDNNFEIPDC LVKLLSAVET PKAWSGFS

UniProtKB: Sakacin-A immunity factor

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Macromolecule #3: Mannose permease IIC component

MacromoleculeName: Mannose permease IIC component / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 25.461646 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DLNFIQVILV IFVAFLAGVE GILDQFHFHQ PVIACTLIGL VTGNLLPCLI LGGTLQMIAL GWANVGAAVA PDAALASIAS AIILVLGGQ GKAGVTSAIA IAVPLAVAGL LLTIIVRTLA TGIVHIMDAA AKEGNFRKIE MWQYIAIIMQ GVRIAIPAGL I LAIGAGPV ...String:
DLNFIQVILV IFVAFLAGVE GILDQFHFHQ PVIACTLIGL VTGNLLPCLI LGGTLQMIAL GWANVGAAVA PDAALASIAS AIILVLGGQ GKAGVTSAIA IAVPLAVAGL LLTIIVRTLA TGIVHIMDAA AKEGNFRKIE MWQYIAIIMQ GVRIAIPAGL I LAIGAGPV KEMLTAMPVW LTDGLAIGGG MVVAVGYAMV INMMATKEVW PFFAIGFVLA TISQLTLIGL GAIGISLALI YL ALSKQGS G

UniProtKB: Mannose permease IIC component

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Macromolecule #4: Mannose permease IID component

MacromoleculeName: Mannose permease IID component / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 33.000723 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QLKLTKKDRI SVWLRSTFLQ GSWNYERMQN GGWAYTLIPA LKKLYKTKED RSAALVRHME FFNTHPYVAA PILGVTLALE EERANGAPI DDVTIQGVKV GMMGPLAGIG DPVFWFTVKP IIGALAASLA MSGNILGPII YFVAWNAIRM AFTWYTQEFG Y RAGSKITE ...String:
QLKLTKKDRI SVWLRSTFLQ GSWNYERMQN GGWAYTLIPA LKKLYKTKED RSAALVRHME FFNTHPYVAA PILGVTLALE EERANGAPI DDVTIQGVKV GMMGPLAGIG DPVFWFTVKP IIGALAASLA MSGNILGPII YFVAWNAIRM AFTWYTQEFG Y RAGSKITE DLSGGILQDI TKGASILGMF ILGSLVNRWV SVKFTPTVSS VKLDKGAFID WDKLPSGAKG IQSALQQQAQ GL SLTDHKI TTLQDNLDSL IPGLAALGLT LFCMWLLKKK VSPIVIILGL FVVGIVFHLL HLM

UniProtKB: Mannose permease IID component

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Macromolecule #5: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178777
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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