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- EMDB-61075: Side fiber of monocin -

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Basic information

Entry
Database: EMDB / ID: EMD-61075
TitleSide fiber of monocin
Map data
Sample
  • Complex: monocin
    • Protein or peptide: Alpha-amylase
    • Protein or peptide: FtbP
    • Protein or peptide: FtbO
    • Protein or peptide: FtbO
  • Ligand: FE (III) ION
KeywordsBacteriocin / bacteriophage / Siphoviridae / F-type tailocin / phage tail-like bacteriocins / Listeria monocytogenes / monocin / cryo-EM / VIRUS LIKE PARTICLE
Function / homologyAlpha-amylase / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsWang JW / Gu ZW
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Nat Commun / Year: 2025
Title: Structure of an F-type phage tail-like bacteriocin from Listeria monocytogenes.
Authors: Zhiwei Gu / Xiaofei Ge / Jiawei Wang /
Abstract: F-type phage tail-like bacteriocins (PTLBs) are high-molecular-weight protein complexes exhibiting bactericidal activity and share evolutionary similarities with the tails of non-contractile ...F-type phage tail-like bacteriocins (PTLBs) are high-molecular-weight protein complexes exhibiting bactericidal activity and share evolutionary similarities with the tails of non-contractile siphoviruses. In this study, we present the atomic structure of monocin, a genetically engineered F-type PTLB from Listeria monocytogenes. Our detailed atomic-level analysis, excluding two chaperone proteins, provides crucial insights into the molecular architecture of F-type PTLBs. The core structure of monocin resembles TP901-1-like phage tails, featuring three side fibers with receptor-binding domains that connect to the baseplate for host adhesion. Based on these findings, we propose a potential mechanism by which F-type PTLBs induce cell death, offering a foundation for developing targeted antibacterial therapies.
History
DepositionAug 5, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61075.png

Downloads & links

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Map

FileDownload / File: emd_61075.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: 0.3
Minimum - Maximum-1.5880378 - 2.7053726
Average (Standard dev.)0.013987019 (±0.10333468)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_61075_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61075_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : monocin

EntireName: monocin
Components
  • Complex: monocin
    • Protein or peptide: Alpha-amylase
    • Protein or peptide: FtbP
    • Protein or peptide: FtbO
    • Protein or peptide: FtbO
  • Ligand: FE (III) ION

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Supramolecule #1: monocin

SupramoleculeName: monocin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Listeria monocytogenes (bacteria)

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Macromolecule #1: Alpha-amylase

MacromoleculeName: Alpha-amylase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 21.669369 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString:
MKLDLWKWEM LLQGREFRNK TNDNWQKLMD WSDFISTGLS AIYVYVNKAD ATLNNKIDTV DKAVNARVNE LISGTEQLSE VVDARSDAF GARYPVLRER LNQEQLNFSK KSTIQFDAST IISMEKQDIG LLTSKKISEA QTVCFLNISS LDEEADIVLE K TGETSFSD NLTSLVFAKI GTNERYQMEP VGA

UniProtKB: Alpha-amylase

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Macromolecule #2: FtbP

MacromoleculeName: FtbP / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 19.783211 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString:
MTKIVKMSEK NEHGTLEQFY PETHAEAVKG LVSVSEEEKT IWDQKESTAG AEQKANTALN SAKDYVDTIG EGTVIFKGAN LMGAGQSFK WDASKLKFGM TLLFSRYDAA NNTPQDYYYH SVFLSKAQLV ELAGKGILVQ MPSTTYGDRK YLYVSTTGLS G HFDNSNYA AWALRQVTIM

UniProtKB: Uncharacterized protein

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Macromolecule #3: FtbO

MacromoleculeName: FtbO / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 17.240197 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString:
MTEIKRMLQT KEDNSKEQFY PETHVAGIVG LTEYVSGQLP TGVVSVNGKA GRVLLDAEDV HAAKKSHTHE VATYTTDGFM SSFDKQKID QLVSPEAGVT SINGKTGIVD LFASDLDAAE INHTHAEATT TESGFLSIDD KEKLDAIQVI ALETIKEVIE

UniProtKB: Uncharacterized protein

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Macromolecule #4: FtbO

MacromoleculeName: FtbO / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 15.772468 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString:
MTEIKRMLQT KEDNSKEQFY PETHVAGIVG LTEYVSGQLP TGVVSVNGKA GRVLLDAEDV HAAKKSHTHE VATYTTDGFM SSFDKQKID QLVSPEAGVT SINGKTGIVD LFASDLDAAE INHTHAEATT TESGFLSIDD KEKLDAI

UniProtKB: Uncharacterized protein

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Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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
VitrificationCryogen name: PROPANE

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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: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43630
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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