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- EMDB-33321: Cryo-EM structure of the bacteriocin-receptor-immunity ternary co... -

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Basic information

Entry
Database: EMDB / ID: EMD-33321
TitleCryo-EM structure of the bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei
Map data
Sample
  • Complex: The bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei
    • Protein or peptide: Bacteriocin sakacin-A
    • Protein or peptide: Mannose permease IIC component
    • Protein or peptide: Mannose permease IID component
    • Protein or peptide: Sakacin-A immunity factor
  • Ligand: alpha-D-mannopyranose
Keywordsantimicrobial peptides / bacteriocins / pediocin-like/class IIa bacteriocins / antibiotic resistance / mannose phosphotransferase / man-PTS / immunity / self-protection / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
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 / 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 sakacin-A / Sakacin-A immunity factor
Similarity search - Component
Biological speciesLatilactobacillus sakei L45 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsWang JW
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171190 China
Ministry of Science and Technology (MoST, China)2016YFA0501103 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
DepositionApr 29, 2022-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33321.png

Downloads & links

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Map

FileDownload / File: emd_33321.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

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8433 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46
Minimum - Maximum-0.8863521 - 2.2929611
Average (Standard dev.)0.019254666 (±0.08471561)
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: Half map 1

Fileemd_33321_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_33321_half_map_2.map
AnnotationHalf map 2
Projections & Slices
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Sample components

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Entire : The bacteriocin-receptor-immunity ternary complex from Lactobacil...

EntireName: The bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei
Components
  • Complex: The bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei
    • Protein or peptide: Bacteriocin sakacin-A
    • Protein or peptide: Mannose permease IIC component
    • Protein or peptide: Mannose permease IID component
    • Protein or peptide: Sakacin-A immunity factor
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: The bacteriocin-receptor-immunity ternary complex from Lactobacil...

SupramoleculeName: The bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Latilactobacillus sakei L45 (bacteria)

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Macromolecule #1: Bacteriocin sakacin-A

MacromoleculeName: Bacteriocin sakacin-A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Latilactobacillus sakei L45 (bacteria)
Molecular weightTheoretical: 4.312893 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARSYGNGVYC NNKKCWVNRG EATQSIIGGM ISGWASGLAG M

UniProtKB: Bacteriocin sakacin-A

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Macromolecule #2: Mannose permease IIC component

MacromoleculeName: Mannose permease IIC component / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Latilactobacillus sakei L45 (bacteria)
Molecular weightTheoretical: 27.467719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDLNFIQVIL VIFVAFLAGV EGILDQFHFH QPVIACTLIG LVTGNLLPCL ILGGTLQMIA LGWANVGAAV APDAALASIA SAIILVLGG QGKAGVTSAI AIAVPLAVAG LLLTIIVRTL ATGIVHIMDA AAKEGNFRKI EMWQYIAIIM QGVRIAIPAG L ILAIGAGP ...String:
MDLNFIQVIL VIFVAFLAGV EGILDQFHFH QPVIACTLIG LVTGNLLPCL ILGGTLQMIA LGWANVGAAV APDAALASIA SAIILVLGG QGKAGVTSAI AIAVPLAVAG LLLTIIVRTL ATGIVHIMDA AAKEGNFRKI EMWQYIAIIM QGVRIAIPAG L ILAIGAGP VKEMLTAMPV WLTDGLAIGG GMVVAVGYAM VINMMATKEV WPFFAIGFVL ATISQLTLIG LGAIGISLAL IY LALSKQG SGNNGGGSNT GDPLGDIIDN Y

UniProtKB: Mannose permease IIC component

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Macromolecule #3: Mannose permease IID component

MacromoleculeName: Mannose permease IID component / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Latilactobacillus sakei L45 (bacteria)
Molecular weightTheoretical: 33.332105 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEQLKLTKK DRISVWLRST FLQGSWNYER MQNGGWAYTL IPALKKLYKT KEDRSAALVR HMEFFNTHPY VAAPILGVTL ALEEERANG APIDDVTIQG VKVGMMGPLA GIGDPVFWFT VKPIIGALAA SLAMSGNILG PIIYFVAWNA IRMAFTWYTQ E FGYRAGSK ...String:
MAEQLKLTKK DRISVWLRST FLQGSWNYER MQNGGWAYTL IPALKKLYKT KEDRSAALVR HMEFFNTHPY VAAPILGVTL ALEEERANG APIDDVTIQG VKVGMMGPLA GIGDPVFWFT VKPIIGALAA SLAMSGNILG PIIYFVAWNA IRMAFTWYTQ E FGYRAGSK ITEDLSGGIL QDITKGASIL GMFILGSLVN RWVSVKFTPT VSSVKLDKGA FIDWDKLPSG AKGIQSALQQ QA QGLSLTD HKITTLQDNL DSLIPGLAAL GLTLFCMWLL KKKVSPIVII LGLFVVGIVF HLLHLM

UniProtKB: Mannose permease IID component

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Macromolecule #4: Sakacin-A immunity factor

MacromoleculeName: Sakacin-A immunity factor / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Latilactobacillus sakei L45 (bacteria)
Molecular weightTheoretical: 13.747889 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKHHHHHHHG AAGTSLYKKA GENLYFQGSM KADYKKINSI LTYTSTALKN PKIIKDKDLV VLLTIIQEEA KQNRIFYDYK RKFRPAVTR FTIDNNFEIP DCLVKLLSAV ETPKAWSGFS

UniProtKB: Sakacin-A immunity factor

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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: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

32031

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 265674
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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