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- EMDB-32030: Cryo-EM structures of Listeria monocytogenes man-PTS -

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Basic information

Entry
Database: EMDB / ID: EMD-32030
TitleCryo-EM structures of Listeria monocytogenes man-PTS
Map data
Sample
  • Complex: mannose-specific PTS system from Listeria monocytogenes
    • Protein or peptide: Mannose/fructose/sorbose family PTS transporter subunit IIC
    • Protein or peptide: PTS mannose family transporter subunit IID
  • Ligand: alpha-D-mannopyranose
Keywordsantimicrobial peptides / bacteriocins / pediocin PA-1 / pediocin-like/class IIa bacteriocins / antibiotic resistance / mannose phosphotransferase / man-PTS / MEMBRANE PROTEIN
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / plasma membrane
Similarity search - Function
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. / :
Similarity search - Domain/homology
PTS mannose family transporter subunit IID / Mannose/fructose/sorbose family PTS transporter subunit IIC
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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 Pore Formation in the Mannose Phosphotransferase System by Pediocin PA-1.
Authors: Liyan Zhu / Jianwei Zeng / Chang Wang / Jiawei Wang /
Abstract: Bacteriocins are ribosomally synthesized bacterial antimicrobial peptides that have a narrow spectrum of antibacterial activity against species closely related to the producers. Pediocin-like (or ...Bacteriocins are ribosomally synthesized bacterial antimicrobial peptides that have a narrow spectrum of antibacterial activity against species closely related to the producers. Pediocin-like (or class IIa) bacteriocins (PLBs) exhibit antibacterial activity against several Gram-positive bacterial strains by forming pores in the cytoplasmic membrane of target cells with a specific receptor, the mannose phosphotransferase system (man-PTS). In this study, we report the cryo-electron microscopy structures of man-PTS from Listeria monocytogenes alone and its complex with pediocin PA-1, the first and most extensively studied representative PLB, at resolutions of 3.12 and 2.45 Å, respectively. The structures revealed that the binding of pediocin PA-1 opens the Core domain of man-PTS away from its Vmotif domain, creating a pore through the cytoplasmic membranes of target cells. During this process, the N-terminal β-sheet region of pediocin PA-1 can specifically attach to the extracellular surface of the man-PTS Core domain, whereas the C-terminal half penetrates the membrane and cracks the man-PTS like a wedge. Thus, our findings shed light on a design of novel PLBs that can kill the target pathogenic bacteria. Listeria monocytogenes is a ubiquitous microorganism responsible for listeriosis, a rare but severe disease in humans, who become infected by ingesting contaminated food products (i.e., dairy, meat, fish, and vegetables): the disease has a fatality rate of 33%. Pediocin PA-1 is an important commercial additive used in food production to inhibit species. The mannose phosphotransferase system (man-PTS) is responsible for the sensitivity of Listeria monocytogenes to pediocin PA-1. In this study, we report the cryo-EM structures of man-PTS from Listeria monocytogenes alone and its complex with pediocin PA-1 at resolutions of 3.12 and 2.45 Å, respectively. Our results facilitate the understanding of the mode of action of class IIa bacteriocins as an alternative to antibiotics.
History
DepositionOct 5, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0167
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0167
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vlx
  • Surface level: 0.0167
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32030.png

Downloads & links

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Map

FileDownload / File: emd_32030.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.995 Å		1.07 Å/pix.
x 256 pix.
= 274.995 Å		1.07 Å/pix.
x 256 pix.
= 274.995 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0167 / Movie #1: 0.0167
Minimum - Maximum-0.04440653 - 0.08862763
Average (Standard dev.)0.00011814679 (±0.0018517203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.9952 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.074199218751.074199218751.07419921875
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z274.995274.995274.995
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0440.0890.000

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Supplemental data

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Sample components

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Entire : mannose-specific PTS system from Listeria monocytogenes

EntireName: mannose-specific PTS system from Listeria monocytogenes
Components
  • Complex: mannose-specific PTS system from Listeria monocytogenes
    • Protein or peptide: Mannose/fructose/sorbose family PTS transporter subunit IIC
    • Protein or peptide: PTS mannose family transporter subunit IID
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: mannose-specific PTS system from Listeria monocytogenes

SupramoleculeName: mannose-specific PTS system from Listeria monocytogenes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Listeria monocytogenes (bacteria)

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Macromolecule #1: Mannose/fructose/sorbose family PTS transporter subunit IIC

MacromoleculeName: Mannose/fructose/sorbose family PTS transporter subunit IIC
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 27.377561 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVISIILVV LIAFLAGIEG ILDEFQFHQP LIACTLIGLV TGNLTACIIL GGTLQMIALG WANIGAAVAP DAALASVASA IILVLGGQG VAGIPSAIAI AIPLAVAGLF LTMIVRTLAV PIVHLMDRAA EKGNIRSVEW LHISAICMQG IRIAIPAAAL L FIPADSVQ ...String:
MSVISIILVV LIAFLAGIEG ILDEFQFHQP LIACTLIGLV TGNLTACIIL GGTLQMIALG WANIGAAVAP DAALASVASA IILVLGGQG VAGIPSAIAI AIPLAVAGLF LTMIVRTLAV PIVHLMDRAA EKGNIRSVEW LHISAICMQG IRIAIPAAAL L FIPADSVQ SFLEAMPAWL TDGMAIGGGM VVAVGYALVI NMMATKEVWP FFVIGFVVAA ISQLTLIAIG ALGVALALIY LN LSKMGGG NSNGGGGGNS RDPLGDILND Y

UniProtKB: Mannose/fructose/sorbose family PTS transporter subunit IIC

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Macromolecule #2: PTS mannose family transporter subunit IID

MacromoleculeName: PTS mannose family transporter subunit IID / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 33.402164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEKIELSKR DRLRVAWRST FIQGSWNYER MQNGGWAFSM IPAIKKLYKT KEDRSSALKR HLEFFNTHPY IASPILGVTL ALEEERANG AEVDDVAIQG VKVGMMGPLA GVGDPVFWFT IRPMLGALGA SLALSGNILG PILFFVAWNV IRWGFMWYTQ E FGYKAGSK ...String:
MAEKIELSKR DRLRVAWRST FIQGSWNYER MQNGGWAFSM IPAIKKLYKT KEDRSSALKR HLEFFNTHPY IASPILGVTL ALEEERANG AEVDDVAIQG VKVGMMGPLA GVGDPVFWFT IRPMLGALGA SLALSGNILG PILFFVAWNV IRWGFMWYTQ E FGYKAGSK ITDDLSGGLL QDITKGASIL GMFVLAALVQ RWVNIQFAPI ISKVKLDEGA YIDWSHLPQG AQGIKTALQQ QQ AGLALSE IKVTTLQNNL DNLIPGLAAV ALTFLCMWLL KKKISPIIII LGLFVVGIVG HLIGLL

UniProtKB: PTS mannose family transporter subunit IID

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Macromolecule #3: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 3 / 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: 7.4
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6k1h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136729
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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