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- EMDB-76176: Escherichia coli MurJ in the outward-facing conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-76176
TitleEscherichia coli MurJ in the outward-facing conformation
Map data
Sample
  • Complex: E. coli MurJ
    • Protein or peptide: Lipid II flippase MurJ
Keywordslipid II flippase / peptidoglycan biosynthesis / TRANSPORT PROTEIN
Function / homology
Function and homology information


glycolipid translocation / 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
Lipid II flippase MurJ
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLi YE / Clemons WM
Funding support United States, 3 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 Foundation United States
Chan Zuckerberg Initiative United States
CitationJournal: J Biol Chem / Year: 2026
Title: Structures of the lipid II flippase from the monoderm pathogen Staphylococcus aureus.
Authors: Yancheng E Li / Grace F Baron / William M Clemons /
Abstract: Peptidoglycan biogenesis requires membrane flippases to translocate lipid-linked precursors across the cytoplasmic membrane for processing. This essential step is mediated by MurJ, the lipid II ...Peptidoglycan biogenesis requires membrane flippases to translocate lipid-linked precursors across the cytoplasmic membrane for processing. This essential step is mediated by MurJ, the lipid II flippase conserved across all peptidoglycan-producing bacteria. While MurJ from diderm bacteria has been structurally resolved in multiple conformational states, its monoderm homolog remains uncharacterized. Monoderm MurJ homologs exhibit substantial sequence divergence yet retain the same lipid II flipping function and are promising antibiotic targets. Here we report structures of Staphylococcus aureus MurJ (SaMurJ) captured in both outward- and inward-facing conformations. These structures show that SaMurJ adopts the conserved MOP family fold and undergoes conformational transitions consistent with an alternating-access mechanism. Our findings reveal conserved and divergent features of MurJ between diderm and monoderm bacteria that are critical for lipid II flipping and provide a structural framework for probing substrate recognition and specific inhibition.
History
DepositionMar 17, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76176.png

Downloads & links

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Map

FileDownload / File: emd_76176.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 480 pix.
= 312. Å		0.65 Å/pix.
x 480 pix.
= 312. Å		0.65 Å/pix.
x 480 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.23830853 - 0.37150723
Average (Standard dev.)0.00022923299 (±0.0049888766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76176_msk_1.map
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Additional map: #1

Fileemd_76176_additional_1.map
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Half map: #1

Fileemd_76176_half_map_1.map
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Half map: #2

Fileemd_76176_half_map_2.map
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Sample components

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Entire : E. coli MurJ

EntireName: E. coli MurJ
Components
  • Complex: E. coli MurJ
    • Protein or peptide: Lipid II flippase MurJ

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Supramolecule #1: E. coli MurJ

SupramoleculeName: E. coli MurJ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 58 KDa

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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: 55.311102 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLLKSLAAV SSMTMFSRVL GFARDAIVAR IFGAGMATDA FFVAFKLPNL LRRIFAEGAF SQAFVPILAE YKSKQGEDAT RVFVSYVSG LLTLALAVVT VAGMLAAPWV IMVTAPGFAD TADKFALTSQ LLKITFPYIL LISLASLVGA ILNTWNRFSI P AFAPTLLN ...String:
MNLLKSLAAV SSMTMFSRVL GFARDAIVAR IFGAGMATDA FFVAFKLPNL LRRIFAEGAF SQAFVPILAE YKSKQGEDAT RVFVSYVSG LLTLALAVVT VAGMLAAPWV IMVTAPGFAD TADKFALTSQ LLKITFPYIL LISLASLVGA ILNTWNRFSI P AFAPTLLN ISMIGFALFA APYFNPPVLA LAWAVTVGGV LQLVYQLPHL KKIGMLVLPR INFHDAGAMR VVKQMGPAIL GV SVSQISL IINTIFASFL ASGSVSWMYY ADRLMEFPSG VLGVALGTIL LPSLSKSFAS GNHDEYNRLM DWGLRLCFLL ALP SAVALG ILSGPLTVSL FQYGKFTAFD ALMTQRALIA YSVGLIGLIV VKVLAPGFYS RQDIKTPVKI AIVTLILTQL MNLA FIGPL KHAGLSLSIG LAACLNASLL YWQLRKQKIF TPQPGWMAFL LRLVVAVLVM SGVLLGMLHI MPEWSLGTMP WRLLR LMAV VLAGIAAYFA ALAVLGFKVK EFARRTV

UniProtKB: Lipid II flippase MurJ

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
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. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 72314
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9nu4


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-11xy:
Escherichia coli MurJ in the outward-facing conformation

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