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- EMDB-64256: JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM) -

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Basic information

Entry
Database: EMDB / ID: EMD-64256
TitleJM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)
Map data
Sample
  • Complex: JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)
    • Protein or peptide: Lipid II flippase MurJ
    • Protein or peptide: Lysis protein
KeywordsPhage / Lysis protein / Complex / VIRAL PROTEIN
Function / homology
Function and homology information


glycolipid translocation / viral release via suppression of host peptidoglycan biosynthetic process / lipid-linked peptidoglycan transport / lipid-linked peptidoglycan transporter activity / division septum / lipid translocation / cardiolipin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane
Similarity search - Function
Peptidoglycan biosynthesis protein MurJ / : / Lipid II flippase MurJ
Similarity search - Domain/homology
Lysis protein / Lipid II flippase MurJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Enterobacteria phage M (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsKohga H / Lertpreedakorn N / Tsukazaki T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Sci Adv / Year: 2025
Title: Phage lysis protein Lys acts as a wedge to block MurJ conformational changes.
Authors: Hidetaka Kohga / Napathip Lertpreedakorn / Ryoji Miyazaki / Sixian Wu / Kaito Hosoda / Hiroyuki Tanaka / Yutaro S Takahashi / Kunihito Yoshikaie / Yutetsu Kuruma / Hideki Shigematsu / ...Authors: Hidetaka Kohga / Napathip Lertpreedakorn / Ryoji Miyazaki / Sixian Wu / Kaito Hosoda / Hiroyuki Tanaka / Yutaro S Takahashi / Kunihito Yoshikaie / Yutetsu Kuruma / Hideki Shigematsu / Takaharu Mori / Tomoya Tsukazaki /
Abstract: Many antibiotics target essential cellular processes. To combat multidrug-resistant bacteria, new antibacterial strategies are needed. In the peptidoglycan biogenesis pathway in , MurJ, the lipid II ...Many antibiotics target essential cellular processes. To combat multidrug-resistant bacteria, new antibacterial strategies are needed. In the peptidoglycan biogenesis pathway in , MurJ, the lipid II flippase, is an essential membrane protein. The 37-residue protein M from the phage, known as Lys or Sgl, targets MurJ and induces cell lysis; however, its molecular mechanism remains unclear. Here, we present the cryo-EM structure of the MurJ/Lys (JM) complex at 3.09-angstrom resolution, revealing that Lys interacts with the crevasse between TM2 and TM7 of MurJ, locking MurJ in an outward-facing conformation, with Lys acting like a wedge. Alanine-scanning mutagenesis and pull-down assays revealed key residues responsible for Lys function, and molecular dynamics simulations showed that Lys stabilizes MurJ's outward-facing state. These findings demonstrate an unprecedented phage-derived mechanism for blocking lipid II transport, providing a structural framework for designing MurJ-targeted antimicrobial agents.
History
DepositionApr 18, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64256.png

Downloads & links

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Map

FileDownload / File: emd_64256.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 256 pix.
= 192.512 Å		0.75 Å/pix.
x 256 pix.
= 192.512 Å		0.75 Å/pix.
x 256 pix.
= 192.512 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.05035188 - 0.11693826
Average (Standard dev.)0.00040155492 (±0.004168752)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 192.512 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64256_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_64256_half_map_2.map
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Sample components

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Entire : JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)

EntireName: JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)
Components
  • Complex: JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)
    • Protein or peptide: Lipid II flippase MurJ
    • Protein or peptide: Lysis protein

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Supramolecule #1: JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)

SupramoleculeName: JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Lipid II flippase MurJ

MacromoleculeName: Lipid II flippase MurJ / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 58.100867 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANLLKSLAA VSSMTMFSRV LGFARDAIVA RIFGAGMATD AFFVAFKLPN LLRRIFAEGA FSQAFVPILA EYKSKQGEDA TRVFVSYVS GLLTLALAVV TVAGMLAAPW VIMVTAPGFA DTADKFALTS QLLKITFPYI LLISLASLVG AILNTWNRFS I PAFAPTLL ...String:
MANLLKSLAA VSSMTMFSRV LGFARDAIVA RIFGAGMATD AFFVAFKLPN LLRRIFAEGA FSQAFVPILA EYKSKQGEDA TRVFVSYVS GLLTLALAVV TVAGMLAAPW VIMVTAPGFA DTADKFALTS QLLKITFPYI LLISLASLVG AILNTWNRFS I PAFAPTLL NISMIGFALF AAPYFNPPVL ALAWAVTVGG VLQLVYQLPH LKKIGMLVLP RINFHDAGAM RVVKQMGPAI LG VSVSQIS LIINTIFASF LASGSVSWMY YADRLMEFPS GVLGVALGTI LLPSLSKSFA SGNHDEYNRL MDWGLRLCFL LAL PSAVAL GILSGPLTVS LFQYGKFTAF DALMTQRALI AYSVGLIGLI VVKVLAPGFY SRQDIKTPVK IAIVTLILTQ LMNL AFIGP LKHAGLSLSI GLAACLNASL LYWQLRKQKI FTPQPGWMAF LLRLVVAVLV MSGVLLGMLH IMPEWSLGTM PWRLL RLMA VVLAGIAAYF AALAVLGFKV KEFARRTVDY KDHDGDYKDH DIDYKDDDDK

UniProtKB: Lipid II flippase MurJ

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Macromolecule #2: Lysis protein

MacromoleculeName: Lysis protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage M (virus)
Molecular weightTheoretical: 5.535437 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYIINLAFC VLLLVAGDSI AYRVSQYLAP LVDTFTKHHH HHHHHHH

UniProtKB: Lysis 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
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: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371016
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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