[English] 日本語
Yorodumi
- EMDB-32031: Cryo-EM structure of Listeria monocytogenes man-PTS complexed wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32031
TitleCryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1
Map data
Sample
  • Complex: Listeria monocytogenes man-PTS complexed with pediocin PA-1
    • Protein or peptide: Mannose/fructose/sorbose family PTS transporter subunit IIC
    • Protein or peptide: PTS mannose family transporter subunit IID
    • Protein or peptide: Bacteriocin pediocin PA-1
  • Ligand: alpha-D-mannopyranose
  • Ligand: water
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 / 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
PTS mannose family transporter subunit IID / Bacteriocin pediocin PA-1 / Mannose/fructose/sorbose family PTS transporter subunit IIC
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria) / Pediococcus acidilactici (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0243
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0243
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7vly
  • Surface level: 0.0243
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32031.png

Downloads & links

-
Map

FileDownload / File: emd_32031.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.)
0.84 Å/pix.
x 256 pix.
= 215.885 Å		0.84 Å/pix.
x 256 pix.
= 215.885 Å		0.84 Å/pix.
x 256 pix.
= 215.885 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8433 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0243 / Movie #1: 0.0243
Minimum - Maximum-0.07917566 - 0.13841036
Average (Standard dev.)0.00016746637 (±0.0034695433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.8848 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.843300781250.843300781250.84330078125
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z215.885215.885215.885
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-0.0790.1380.000

-
Supplemental data

-
Sample components

-
Entire : Listeria monocytogenes man-PTS complexed with pediocin PA-1

EntireName: Listeria monocytogenes man-PTS complexed with pediocin PA-1
Components
  • Complex: Listeria monocytogenes man-PTS complexed with pediocin PA-1
    • Protein or peptide: Mannose/fructose/sorbose family PTS transporter subunit IIC
    • Protein or peptide: PTS mannose family transporter subunit IID
    • Protein or peptide: Bacteriocin pediocin PA-1
  • Ligand: alpha-D-mannopyranose
  • Ligand: water

-
Supramolecule #1: Listeria monocytogenes man-PTS complexed with pediocin PA-1

SupramoleculeName: Listeria monocytogenes man-PTS complexed with pediocin PA-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Listeria monocytogenes (bacteria)

-
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

-
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

-
Macromolecule #3: Bacteriocin pediocin PA-1

MacromoleculeName: Bacteriocin pediocin PA-1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pediococcus acidilactici (bacteria)
Molecular weightTheoretical: 5.001667 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PHMKYYGNGV TCGKHSCSVD WGKATTCIIN NGAMAWATGG HQGNHKC

UniProtKB: Bacteriocin pediocin PA-1

-
Macromolecule #4: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 30 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

-
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: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vlx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 659531
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more