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

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Basic information

Entry
Database: PDB / ID: 9nu4
TitleStructure of MurJ in complex with single gene lysis protein from phage M
Components
  • Lipid II flippase MurJ
  • Lysis protein
KeywordsTRANSPORT PROTEIN / lipid II flippase / phage single gene lysis proteins / peptidoglycan biosynthesis
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi, Y.E. / Clemons, W.M.
Funding support United States, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipid II flippase MurJ
B: Lysis protein


Theoretical massNumber of molelcules
Total (without water)73,2942
Polymers73,2942
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 Lipid II flippase MurJ / Peptidoglycan biosynthesis protein MurJ


Mass: 66668.680 Da / Num. of mol.: 1 / Mutation: K5F, S12I, M13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: murJ, mviN, yceN, b1069, JW1056 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AF16
#2: Protein Lysis protein


Mass: 6625.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M (virus) / Gene: lys / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K7QK87
Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1MurJ in complex with single gene lysis protein from phage MCOMPLEXall0MULTIPLE SOURCES
2soluble cytochrome b562, lipid II flippase MurJ fusionCOMPLEX#11RECOMBINANT
3single gene lysis protein from phage MCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.0732 MDaNO
210.0666 MDaNO
310.0066 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli K-12 (bacteria)83333
23Enterobacteria phage M (virus)1235640
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli BL21(DE3) (bacteria)469008
23Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMSodium chlorideNaCl1
35 %GlycerolC3H8O31
40.005 %LMNGC47H88O221
50.0005 %CHSC31H50O41
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2SerialEM4.1.1image acquisition
4cryoSPARC4.5.3CTF correction
7Coot0.9.8model fitting
9PHENIX1.21_5207model refinement
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61237 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16CC4

6cc4

16CC41PDBexperimental model
21AF-P0AF16-F1-v42AlphaFoldin silico model
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0064931
ELECTRON MICROSCOPYf_angle_d0.7036708
ELECTRON MICROSCOPYf_dihedral_angle_d3.996669
ELECTRON MICROSCOPYf_chiral_restr0.044805
ELECTRON MICROSCOPYf_plane_restr0.006827

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