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- EMDB-61073: Cap region of monocin -

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Basic information

Entry
Database: EMDB / ID: EMD-61073
TitleCap region of monocin
Map data
Sample
  • Complex: monocin
    • Protein or peptide: AA protein
    • Protein or peptide: DUF5072 domain-containing protein
KeywordsBacteriocin / bacteriophage / Siphoviridae / F-type tailocin / phage tail-like bacteriocins / Listeria monocytogenes / monocin / cryo-EM / VIRUS LIKE PARTICLE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 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-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61073.png

Downloads & links

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Map

FileDownload / File: emd_61073.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 322.26 Å		1.07 Å/pix.
x 300 pix.
= 322.26 Å		1.07 Å/pix.
x 300 pix.
= 322.26 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: 0.32
Minimum - Maximum-0.44973907 - 1.1178113
Average (Standard dev.)0.0015617987 (±0.05268705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 322.26 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61073_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61073_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : monocin

EntireName: monocin
Components
  • Complex: monocin
    • Protein or peptide: AA protein
    • Protein or peptide: DUF5072 domain-containing protein

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Supramolecule #1: monocin

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

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Macromolecule #1: AA protein

MacromoleculeName: AA protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 18.01026 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString:
MAFEENLYCD YTPGAAKAVA GKDVILAVFN AAGDKLLAVA GQQGLTVNRS KDSIEITSKD TVGGWKSKIG GMKEWSIEND GLYVADAES HKELAKYFES DSPVCVKIIN QASKKGLFGG LAIVADYSFE APFDEAMTYS VKLDGMGALV DLTITEGGDQ M PGETPVAP AE

UniProtKB: AA protein

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Macromolecule #2: DUF5072 domain-containing protein

MacromoleculeName: DUF5072 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 14.966455 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString:
MKSLSFMRVL EAVRTMLQEK GGLDVSIVMR NQVEMPTTMI EMIDQEEEES QTAWKEKYRF AIHHYTNEQD LAGVEKIDTL IQMGFILPE GYKLVAVRHC GKQNLVKENT LIHAKTSFEV SICRELKVKI

UniProtKB: DUF5072 domain-containing protein

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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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13473
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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