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Yorodumi- EMDB-34726: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34726 | |||||||||
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Title | The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information protein-Npi-phosphohistidine-sugar phosphotransferase / protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity / bacteriocin immunity / cytolysis / phosphoenolpyruvate-dependent sugar phosphotransferase system / defense response to bacterium / host cell plasma membrane / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Lactococcus lactis subsp. lactis (strain KF147) (lactic acid bacteria) / Lactococcus lactis subsp. lactis (lactic acid bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.98 Å | |||||||||
Authors | Wang JW | |||||||||
Funding support | China, 1 items
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Citation | Journal: Appl Environ Microbiol / Year: 2023 Title: Structural Basis of the Mechanisms of Action and Immunity of Lactococcin A, a Class IId Bacteriocin. Authors: Ruilian Li / Jinsong Duan / Yicheng Zhou / Jiawei Wang / Abstract: Lactococcin A (LcnA), a class IId bacteriocin, induces membrane leakage and cell death by specifically binding to the membrane receptor-mannose phosphotransferase system (man-PTS), as is the case for ...Lactococcin A (LcnA), a class IId bacteriocin, induces membrane leakage and cell death by specifically binding to the membrane receptor-mannose phosphotransferase system (man-PTS), as is the case for pediocin-like (class IIa) bacteriocins. The cognate immunity protein of bacteriocins, which protects the producer cell from its own bacteriocin, recognizes and binds to the bacteriocin-man-PTS complex, consequently blocking membrane leakage. We previously deciphered the mode of action and immunity of class IIa bacteriocins. Here, we determined the structure of the ternary complex of LcnA, LciA (, the immunity protein), and its receptor, , the man-PTS of Lactococcus lactis (ll-man-PTS). An external loop on the membrane-located component IIC of ll-man-PTS was found to prevent specific binding of the N-terminal region of LcnA to the site recognized by pediocin-like bacteriocins. Thus, the N-terminal β-sheet region of LcnA recognized an adjacent site on the extracellular side of ll-man-PTS, with the LcnA C-terminal hydrophobic helix penetrating into the membrane. The cytoplasmic cleft formed within the man-PTS Core and Vmotif domains induced by embedded LcnA from the periplasmic side is adopted by the appropriate angle between helices H3 and H4 of the N terminus of LciA. The flexible C terminus of LciA then blocks membrane leakage. To summarize, our findings reveal the molecular mechanisms of action and immunity of LcnA and LciA, laying a foundation for further design of class IId bacteriocins. Class IId (lactococcin-like) bacteriocins and class IIa (pediocin-like) bacteriocins share a few similarities: (i) both induce membrane leakage and cell death by specifically binding the mannose phosphotransferase system (man-PTS) on their target cells, and (ii) cognate immunity proteins recognize and bind to the bacteriocin-man-PTS complex to block membrane leakage. However, class IId bacteriocins lack the "pediocin box" motif, which is typical of class IIa bacteriocins, and basically target only lactococcal cells; in contrast, class IIa bacteriocins target diverse bacterial cells, but not lactococcal cells. We previously solved the structure of class IIa bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei. Here, we determined the structure of the ternary complex of class IId bacteriocin LcnA, its cognate immunity protein LciA, and its receptor, the man-PTS of Lactococcus lactis. By comparing the interactions between man-PTS and class IIa and class IId bacteriocins, this study affords some clues to better understand the specificity of bacteriocins targeting the mannose phosphotransferase system. #1: Journal: Applied and Environmental Microbiology / Year: 2023 Title: Structural Basis of the Mechanisms of Action and Immunity of Lactococcin A, a Class IId Bacteriocin Authors: Li R / Duan J / Zhou Y / Wang J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34726.map.gz | 6.5 MB | EMDB map data format | |
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Header (meta data) | emd-34726-v30.xml emd-34726.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34726_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_34726.png | 92.3 KB | ||
Others | emd_34726_half_map_1.map.gz emd_34726_half_map_2.map.gz | 49.5 MB 49.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34726 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34726 | HTTPS FTP |
-Related structure data
Related structure data | 8hfsMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34726.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0742 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 1
File | emd_34726_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_34726_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis
Entire | Name: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis |
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Components |
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-Supramolecule #1: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis
Supramolecule | Name: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Lactococcus lactis subsp. lactis (strain KF147) (lactic acid bacteria) |
-Macromolecule #1: Mannose-specific PTS system, IIC component
Macromolecule | Name: Mannose-specific PTS system, IIC component / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO EC number: protein-Npi-phosphohistidine-sugar phosphotransferase |
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Source (natural) | Organism: Lactococcus lactis subsp. lactis (strain KF147) (lactic acid bacteria) |
Molecular weight | Theoretical: 27.572371 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEYGVLSVIL VIVVAFLAGL EGILDQWQFH QPIIACSLIG IVTGHASAGI ILGGSLQLIA LGWANVGAAV APDAALASIA SSILMVQSN NFDLTHIMGT IVPAAILLAT AGLVLTTLVR MLSVVLVHQA DRAAENGSYS GVEMWHFIAL ICQGLRIAIP A GLLLVISP ...String: MEYGVLSVIL VIVVAFLAGL EGILDQWQFH QPIIACSLIG IVTGHASAGI ILGGSLQLIA LGWANVGAAV APDAALASIA SSILMVQSN NFDLTHIMGT IVPAAILLAT AGLVLTTLVR MLSVVLVHQA DRAAENGSYS GVEMWHFIAL ICQGLRIAIP A GLLLVISP DAIQKALAAI PPVISGGLAV GGGMVVAVGY AMVINLMATR EVWPFFFLGF ALAPISELTL IATGVLGVVI AI VYLNLQA SGGSGNGTAS SSGDPIGDIL NDY |
-Macromolecule #2: Mannose-specific PTS system, IID component
Macromolecule | Name: Mannose-specific PTS system, IID component / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO EC number: protein-Npi-phosphohistidine-sugar phosphotransferase |
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Source (natural) | Organism: Lactococcus lactis subsp. lactis (strain KF147) (lactic acid bacteria) |
Molecular weight | Theoretical: 33.630473 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSENKVTLDK KIRRSVMWRS MFLQGSWNYE RMQNGGWAYS LIPALKKLYP SGEEAKEALK RHLEFFNTHP YVAAPIIGVT LALEEERAN GADIDDAAIQ GVKVGMMGPL AGIGDPVFWF TVRPIVGAIA ASLATGGSII APLFFFIVWN AIRIAFLWYT Q EFGYKSGS ...String: MSENKVTLDK KIRRSVMWRS MFLQGSWNYE RMQNGGWAYS LIPALKKLYP SGEEAKEALK RHLEFFNTHP YVAAPIIGVT LALEEERAN GADIDDAAIQ GVKVGMMGPL AGIGDPVFWF TVRPIVGAIA ASLATGGSII APLFFFIVWN AIRIAFLWYT Q EFGYKSGS AITKDLGGGL LQTVTKGASI LGMFVLGVLI QRWVTINFNG PNAVVSKIPL QKGAYVEFPK GSVSGTQLHD IL GQVGNKL SLDPTKVTYL QDNLNQLIPG LAGLLITLLC MWLLKKKVSP IVIIFGLFVV GILGRWAQIM |
-Macromolecule #3: Lactococcin-A immunity protein
Macromolecule | Name: Lactococcin-A immunity protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lactococcus lactis subsp. lactis (lactic acid bacteria) |
Molecular weight | Theoretical: 11.179947 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKKKQIEFEN ELRSMLATAL EKDISQEERN ALNIAEKALD NSEYLPKIIL NLRKALTPLA INRTLNHDLS ELYKFITSSK ASNKNLGGG LIMSWGRLF |
-Macromolecule #4: Bacteriocin lactococcin-A
Macromolecule | Name: Bacteriocin lactococcin-A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lactococcus lactis subsp. lactis (lactic acid bacteria) |
Molecular weight | Theoretical: 5.783341 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: KLTFIQSTAA GDLYYNTNTH KYVYQQTQNA FGAAANTIVN GWMGGAAGGF GLHH |
-Macromolecule #5: alpha-D-mannopyranose
Macromolecule | Name: alpha-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: MAN |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ChemComp-MAN: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-8hfs: |