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- EMDB-61074: Tip region of monocin -

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Basic information

Entry
Database: EMDB / ID: EMD-61074
TitleTip region of monocin
Map data
Sample
  • Complex: monocin
    • Protein or peptide: AA protein
    • Protein or peptide: FtbJ
    • Protein or peptide: FtbK
    • Protein or peptide: FtbL
    • Protein or peptide: CCA-adding enzyme
KeywordsBacteriocin / bacteriophage / Siphoviridae / F-type tailocin / phage tail-like bacteriocins / Listeria monocytogenes / monocin / cryo-EM / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


Prophage endopeptidase tail, N-terminal / Prophage endopeptidase tail N-terminal domain / Prophage tail endopeptidase / Prophage endopeptidase tail / Siphovirus-type tail component / Phage tail protein RIFT-related domain / Phage major tail protein TP901-1 / Phage tail tube protein / Armadillo-type fold
Similarity search - Domain/homology
CCA-adding enzyme / FtbJ / FtbL / FtbK / AA protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 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_61074.png

Downloads & links

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Map

FileDownload / File: emd_61074.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 549.99 Å		1.07 Å/pix.
x 512 pix.
= 549.99 Å		1.07 Å/pix.
x 512 pix.
= 549.99 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: 0.23
Minimum - Maximum-0.50309724 - 1.7631584
Average (Standard dev.)0.00036040074 (±0.05955037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 549.9904 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61074_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_61074_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: FtbJ
    • Protein or peptide: FtbK
    • Protein or peptide: FtbL
    • Protein or peptide: CCA-adding enzyme

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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: 30 / 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: FtbJ

MacromoleculeName: FtbJ / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 65.312633 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString: MAESKSITFE LNESVLTAQV GRLDEMAMVV ERRFSELKMT IEDVGNADPG SKISESLGGL QSGLGTISSA FGQLGSSSEA ITSGFGTAV GSVGGITDAF KNLGSSVQNG TLFSSLATGI GGMSTMLGGV SGGVQGITNL ASGFMELKNH LGGLMSSIGG V GGIMGKLT ...String:
MAESKSITFE LNESVLTAQV GRLDEMAMVV ERRFSELKMT IEDVGNADPG SKISESLGGL QSGLGTISSA FGQLGSSSEA ITSGFGTAV GSVGGITDAF KNLGSSVQNG TLFSSLATGI GGMSTMLGGV SGGVQGITNL ASGFMELKNH LGGLMSSIGG V GGIMGKLT SPMGLVIIGI VALVAAFTYL MTTNESFRNT VMSVVTQVAQ LFGQLVASLM PIIMQIVTAV MQIGAALMPM VM QFISFFA QLLAQLMPFI NMLISMLMPV IMQIVQVVMS LVSALLPSIM TVIQGIMSVI QFLIPIIMQI ATVVVQIVVT IIS YISKIM PIVMTIIGVI VSIITTIISY VVIIATTIAS VIGKIISFIA SVITAVIGIV QPIIAFITNI FTTIVTIIGA AFQM VFTVA SKIWNSIMST ISGIIDGIKA VITGISTTVS SVFNGVKRII TGVFDGIKSA WGGLTDFVGN IFDGVSSAIQ TVVDN VKGF VNVVIRGING AIGLINKIPG VEIGKIPQLI SGTTNFQGGF ARMNEGGRGE MVVLPSGSQV IPHDATMKYA RESARG NKS MLYTSQGADL ARVENLLERL LQKNPVIKMD DKVVAEVVSR NQANSFDQYN YTMGGAAYS

UniProtKB: FtbJ

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Macromolecule #3: FtbK

MacromoleculeName: FtbK / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 31.37335 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString: MSDLFLELNG KVHSLSETFP GLSVQEVSRQ SPQLSMETAE IAGTDGVIPG MTQFKPFIFS AKCNLQALDI PDYHLAVREI YEFLFQRDS YYIWSDQMPG IRYEVHPKPV DFSRESDRVG LLTIEFDVFK GYAESRGTSL DPMTFEVDLW QMGMNLSNRD D LFYVFREN ...String:
MSDLFLELNG KVHSLSETFP GLSVQEVSRQ SPQLSMETAE IAGTDGVIPG MTQFKPFIFS AKCNLQALDI PDYHLAVREI YEFLFQRDS YYIWSDQMPG IRYEVHPKPV DFSRESDRVG LLTIEFDVFK GYAESRGTSL DPMTFEVDLW QMGMNLSNRD D LFYVFREN TFRVYNAGSD RVNPLMRHEL DIAMTANGTP TIHNLTTGES FEYRKELQKT DVLLLNNIYP LVNNRRVGKD TN HGIITLE KGWNDFEIKG VTDVTIAFNF PFIYR

UniProtKB: FtbK

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Macromolecule #4: FtbL

MacromoleculeName: FtbL / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 43.228668 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString: MDYVIIQSMD KEVEEILTDI DYGSFSYDYE KNTSRAISFT VNKTKQNAAI FDLVGNEAIL TYQGQQFVIK KCTPKSIGGT ISKQITAQH ICYTVQDHVQ YNVKSGRKKY SIQTVLEFAL QDNVLGFSYE IQGSFPLVEL EDLGNKNGLE LVNLCLEEFG A ILFADNKK ...String:
MDYVIIQSMD KEVEEILTDI DYGSFSYDYE KNTSRAISFT VNKTKQNAAI FDLVGNEAIL TYQGQQFVIK KCTPKSIGGT ISKQITAQH ICYTVQDHVQ YNVKSGRKKY SIQTVLEFAL QDNVLGFSYE IQGSFPLVEL EDLGNKNGLE LVNLCLEEFG A ILFADNKK LYFYDEKSWY VRTEKQFRYL YNTEEVSVDT NTDNLKTEIK CYGKQKENAD KLTGDNKYMA VVTYTSPNEA IY GKRMANA KSDDKITNND DLLIFAKKQI LDVPETALTI AYKGKEPVSE RDVWYFIHEP MGFETEVKVT KIKSSHPWSK KFQ EIGFSN SRRDMVRIQT QIANQVKKAS VDTNKINSFS SIAMNAYDSR ILTEVVGVVD GD

UniProtKB: FtbL

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Macromolecule #5: CCA-adding enzyme

MacromoleculeName: CCA-adding enzyme / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 10.635911 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString:
MATEIRVLKN VDDTVFYPKT HVTAVEGLDS ATTTTSGLMP ASDKTKLNGI EANAEKNNVT AIDIANWNKK QDAILVSENG SNFKITVTN AGELKATKVE

UniProtKB: CCA-adding enzyme

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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: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44283
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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