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- PDB-9j1j: Cap region of monocin -

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Basic information

Entry
Database: PDB / ID: 9j1j
TitleCap region of monocin
Components
  • AA protein
  • DUF5072 domain-containing protein
KeywordsVIRUS LIKE PARTICLE / Bacteriocin / bacteriophage / Siphoviridae / F-type tailocin / phage tail-like bacteriocins / Listeria monocytogenes / monocin / cryo-EM
Function / homologyPutative tail termination protein / : / Phage major tail protein TP901-1 / Phage tail tube protein / DUF5072 domain-containing protein / AA protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 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
G: AA protein
g: AA protein
F: DUF5072 domain-containing protein
A: DUF5072 domain-containing protein
B: AA protein
C: AA protein
D: DUF5072 domain-containing protein
E: AA protein
H: AA protein
I: DUF5072 domain-containing protein
J: AA protein
K: AA protein
L: DUF5072 domain-containing protein
M: AA protein
N: AA protein
O: DUF5072 domain-containing protein
P: AA protein
Q: AA protein


Theoretical massNumber of molelcules
Total (without water)305,92218
Polymers305,92218
Non-polymers00
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
AA protein / FtbG / Antigen A / Phage major tail protein / TP901-1 family


Mass: 18010.260 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: lmaA, aA, A7H14_01990, A8L61_07680, AB917_02055, ABZ57_09930, AF817_12225, AP104_04170, APD71_11000, APD94_11395, ART25_13165, ARY78_13740, B1N52_06345, B4X68_12550, B5K54_07765, BB997_05830, ...Gene: lmaA, aA, A7H14_01990, A8L61_07680, AB917_02055, ABZ57_09930, AF817_12225, AP104_04170, APD71_11000, APD94_11395, ART25_13165, ARY78_13740, B1N52_06345, B4X68_12550, B5K54_07765, BB997_05830, BCZ19_12960, BCZ21_05430, CAV64_13840, CD20_13395, CW845_05245, CW895_09010, D4271_13110, D4920_13625, D4B11_08575, D4C60_14745, D4D89_13045, D4U23_07845, D5M70_13180, D5N24_12985, D7104_05135, DCT16_05880, DG57_02025, DQ70_12600, DU018_08360, E0I30_13015, E0I39_12940, E1V33_11285, E1W56_14335, E5F58_14110, EX365_09125, EXZ73_03465, EYJ21_12355, EZM42_13115, F1788_11005, F3300_10015, F6436_02005, F6515_08425, FA835_09655, FJL03_10525, FJU19_13205, FLQ76_11460, FLQ91_11040, FLQ97_00985, FNX40_02305, FPL45_04450, FV747_02065, G3O21_000404, G3R95_002798, G3R97_002705, GCV64_11950, GHH22_14070, GHO09_06915, GJW51_04795, GQG13_06300, GT011_12400, GYO01_10490, GYP27_04130, GYR60_10835, GYS09_07335, GYU24_12575, GYX23_01965, GYY14_04840, GZK27_10205, KV70_02000, QD52_06145
Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: O05551
#2: Protein
DUF5072 domain-containing protein / FtbF


Mass: 14966.455 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: AP104_04165, B4X68_12545 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A9P1T1V5
Has protein modificationY

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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: all / 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

CTF correctionType: NONE
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13473 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00420244
ELECTRON MICROSCOPYf_angle_d0.73727258
ELECTRON MICROSCOPYf_dihedral_angle_d5.0372724
ELECTRON MICROSCOPYf_chiral_restr0.0483090
ELECTRON MICROSCOPYf_plane_restr0.0043486

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