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- EMDB-49796: Structure of MurJ in complex with single gene lysis protein from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-49796
TitleStructure of MurJ in complex with single gene lysis protein from phage M
Map data
Sample
  • Complex: MurJ in complex with single gene lysis protein from phage M
    • Complex: soluble cytochrome b562, lipid II flippase MurJ fusion
      • Protein or peptide: Lipid II flippase MurJ
    • Complex: single gene lysis protein from phage M
      • Protein or peptide: Lysis protein
Keywordslipid II flippase / phage single gene lysis proteins / peptidoglycan biosynthesis / TRANSPORT 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 K-12 (bacteria) / Enterobacteria phage M (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi YE / Clemons WM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114611 United States
The G. Harold and Leila Y. Mathers Foundationto W.M.C. United States
CitationJournal: Nature / Year: 2026
Title: Convergent MurJ flippase inhibition by phage lysis proteins.
Authors: Yancheng E Li / S Francesca Antillon / Grace F Baron / Karthik Chamakura / Ry Young / William M Clemons /
Abstract: Antimicrobial drug resistance poses a global health challenge that necessitates the identification of new druggable targets. The essential lipid II flippase MurJ is a promising yet underexplored ...Antimicrobial drug resistance poses a global health challenge that necessitates the identification of new druggable targets. The essential lipid II flippase MurJ is a promising yet underexplored antimicrobial target in bacterial cell wall biosynthesis. The only known inhibitors of Gram-negative (diderm) MurJ are the single-gene lysis proteins (Sgls) from the lytic single-strand RNA phages M (Sgl) and PP7 (Sgl). Sgl and Sgl have distinct evolutionary origins and share no sequence similarity. Here we describe a common mechanism of MurJ inhibition by these phage-encoded Sgls. We determined the structures of MurJ-bound Sgl and Sgl and discovered a third distinct MurJ-targeting Sgl from the predicted phage Changjiang3 (Sgl) that we also characterized structurally. Our findings demonstrate that all three Sgls evolved convergently to trap MurJ in a periplasm-open conformation through a common MurJ interface, revealing a pathway for drug design.
History
DepositionMar 19, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49796.png

Downloads & links

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Map

FileDownload / File: emd_49796.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.)
0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.29839304 - 0.44351688
Average (Standard dev.)0.00016922556 (±0.0053531434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49796_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_49796_additional_1.map
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Half map: #2

Fileemd_49796_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_49796_half_map_2.map
Projections & Slices
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Sample components

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Entire : MurJ in complex with single gene lysis protein from phage M

EntireName: MurJ in complex with single gene lysis protein from phage M
Components
  • Complex: MurJ in complex with single gene lysis protein from phage M
    • Complex: soluble cytochrome b562, lipid II flippase MurJ fusion
      • Protein or peptide: Lipid II flippase MurJ
    • Complex: single gene lysis protein from phage M
      • Protein or peptide: Lysis protein

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Supramolecule #1: MurJ in complex with single gene lysis protein from phage M

SupramoleculeName: MurJ in complex with single gene lysis protein from phage M
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 6.6 KDa

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Supramolecule #2: soluble cytochrome b562, lipid II flippase MurJ fusion

SupramoleculeName: soluble cytochrome b562, lipid II flippase MurJ fusion
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Supramolecule #3: single gene lysis protein from phage M

SupramoleculeName: single gene lysis protein from phage M / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Enterobacteria phage M (virus)

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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 K-12 (bacteria)
Molecular weightTheoretical: 66.66868 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MADLEDNWET LNDNLKVIEK ADNAAQVKDA LTKMRAAALD AQKATPPKLE DKSPDSPEMK DFRHGFDILV GQIDDALKLA NEGKVKEAQ AAAEQLKTTR NAYIQKYLLF SLAAVSIATM FSRVLGFARD AIVARIFGAG MATDAFFVAF KLPNLLRRIF A EGAFSQAF ...String:
MADLEDNWET LNDNLKVIEK ADNAAQVKDA LTKMRAAALD AQKATPPKLE DKSPDSPEMK DFRHGFDILV GQIDDALKLA NEGKVKEAQ AAAEQLKTTR NAYIQKYLLF SLAAVSIATM FSRVLGFARD AIVARIFGAG MATDAFFVAF KLPNLLRRIF A EGAFSQAF VPILAEYKSK QGEDATRVFV SYVSGLLTLA LAVVTVAGML AAPWVIMVTA PGFADTADKF ALTSQLLKIT FP YILLISL ASLVGAILNT WNRFSIPAFA PTLLNISMIG FALFAAPYFN PPVLALAWAV TVGGVLQLVY QLPHLKKIGM LVL PRINFH DAGAMRVVKQ MGPAILGVSV SQISLIINTI FASFLASGSV SWMYYADRLM EFPSGVLGVA LGTILLPSLS KSFA SGNHD EYNRLMDWGL RLCFLLALPS AVALGILSGP LTVSLFQYGK FTAFDALMTQ RALIAYSVGL IGLIVVKVLA PGFYS RQDI KTPVKIAIVT LILTQLMNLA FIGPLKHAGL SLSIGLAACL NASLLYWQLR KQKIFTPQPG WMAFLLRLVV AVLVMS GVL LGMLHIMPEW SLGTMPWRLL RLMAVVLAGI AAYFAALAVL GSAWSHPQFE K

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: 6.625324 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGHHHHHHGS GSGSGSGSGS GSGSGSGSGS KYIINLAFCV LLLVAGDSIA YRVSQYLAPL VDTFTK

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

Concentration4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloride
5.0 %C3H8O3Glycerol
0.005 %C47H88O22LMNG
0.0005 %C31H50O4CHS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 61237
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6cc4

source_name: PDB, initial_model_type: experimental model

1-v4

source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL
Output model

PDB-9nu4:
Structure of MurJ in complex with single gene lysis protein from phage M

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