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- PDB-9j1l: Side fiber of monocin -

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Basic information

Entry
Database: PDB / ID: 9j1l
TitleSide fiber of monocin
Components
  • (FtbO) x 2
  • Alpha-amylase
  • FtbP
KeywordsVIRUS LIKE PARTICLE / Bacteriocin / bacteriophage / Siphoviridae / F-type tailocin / phage tail-like bacteriocins / Listeria monocytogenes / monocin / cryo-EM
Function / homology: / Alpha-amylase / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsWang, J.W. / Gu, Z.W.
Funding support China, 2items
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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Alpha-amylase
2: FtbP
3: FtbO
A: FtbP
B: FtbP
C: FtbP
I: FtbP
N: Alpha-amylase
O: FtbO
P: FtbP
Q: FtbP
R: FtbP
n: Alpha-amylase
o: FtbO
p: FtbP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,42217
Polymers293,31015
Non-polymers1122
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Alpha-amylase / FtbN


Mass: 21669.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AF817_12260, AP104_04205, B4X68_12585, DG57_02060, EYJ21_12320, F1788_11040, FJL03_10560, GCV64_11985, GT011_12435, GYO01_10525, GYP27_04165, GYU24_12610, GZK27_10240
Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A3D7WJE9
#2: Protein
FtbP


Mass: 19783.211 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AF817_12270, AP104_04215, B4X68_12595, DG57_02070, EYJ21_12310, EZM42_13160, F1788_11050, FJL03_10570, FPL45_04495, GHO09_06960, GT011_12445, GYO01_10535, GYP27_04175, GYU24_12620, GZK27_10250
Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A3R0H0Z2
#3: Protein FtbO


Mass: 17240.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AP104_04210, B4X68_12590, EYJ21_12315, EZM42_13155, F1788_11045, FJL03_10565, FPL45_04490, GCV64_11990, GHO09_06955, GYO01_10530, GYP27_04170, GZK27_10245
Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A3T2E047
#4: Protein FtbO


Mass: 15772.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: AP104_04210, B4X68_12590, EYJ21_12315, EZM42_13155, F1788_11045, FJL03_10565, FPL45_04490, GCV64_11990, GHO09_06955, GYO01_10530, GYP27_04170, GZK27_10245
Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A3T2E047
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: monocin / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Listeria monocytogenes (bacteria)
Source (recombinant)Organism: Lactococcus lactis (lactic acid bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43630 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00820658
ELECTRON MICROSCOPYf_angle_d0.91227915
ELECTRON MICROSCOPYf_dihedral_angle_d4.2712751
ELECTRON MICROSCOPYf_chiral_restr0.0413132
ELECTRON MICROSCOPYf_plane_restr0.0033564

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