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- EMDB-76178: Staphylococcus aureus MurJ R176A mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-76178
TitleStaphylococcus aureus MurJ R176A mutant
Map data
Sample
  • Complex: Staphylococcus aureus MurJ R176A mutant
    • Protein or peptide: Polysaccharide biosynthesis protein, putative
Keywordslipid II flippase / peptidoglycan biosynthesis / TRANSPORT PROTEIN
Function / homologyPeptidoglycan biosynthesis protein, SpoVB-type / Polysaccharide biosynthesis protein / : / Polysaccharide biosynthesis protein / plasma membrane / Polysaccharide biosynthesis protein, putative
Function and homology information
Biological speciesStaphylococcus aureus (bacteria) / Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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 Foundationto W.M.C. 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_76178.png

Downloads & links

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Map

FileDownload / File: emd_76178.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 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
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Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3726095 - 0.49321356
Average (Standard dev.)0.000114625924 (±0.0079378225)
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_76178_msk_1.map
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Additional map: #1

Fileemd_76178_additional_1.map
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Half map: #1

Fileemd_76178_half_map_1.map
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Half map: #2

Fileemd_76178_half_map_2.map
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Sample components

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Entire : Staphylococcus aureus MurJ R176A mutant

EntireName: Staphylococcus aureus MurJ R176A mutant
Components
  • Complex: Staphylococcus aureus MurJ R176A mutant
    • Protein or peptide: Polysaccharide biosynthesis protein, putative

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Supramolecule #1: Staphylococcus aureus MurJ R176A mutant

SupramoleculeName: Staphylococcus aureus MurJ R176A mutant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 66 KDa

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Macromolecule #1: Polysaccharide biosynthesis protein, putative

MacromoleculeName: Polysaccharide biosynthesis protein, putative / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47
Molecular weightTheoretical: 61.912188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSESKEMVRG TFLITISILI TKVLGVLFII PFNYLIGGQE NMAPFTYAYA PYNIAIAVAT AGVPLAASKY VAKYNAIGAY KVSQKFYKS SFIVMSITGV LGFLVLYFLA PYISELTLAR NIHDKNGWSV DDITWIIRII SMVVIFIPVL ATWRGIFQGY K SMGPTAVS ...String:
MSESKEMVRG TFLITISILI TKVLGVLFII PFNYLIGGQE NMAPFTYAYA PYNIAIAVAT AGVPLAASKY VAKYNAIGAY KVSQKFYKS SFIVMSITGV LGFLVLYFLA PYISELTLAR NIHDKNGWSV DDITWIIRII SMVVIFIPVL ATWRGIFQGY K SMGPTAVS EVTEQIAAVI FILIGSYLVL NVFDGSILLA NGIATFAAAV GAIIGIFTLW YYWRKRKHNI DRMVESDYTD ID VSYGKMY KEIIAYSIPF VIVSLNYPLF NLVDQFTHNG ALSLVGIPSQ LQDIFFNMLN MSTNKIVMIP TSLSAGFAVS LIP YITKTF AEGRLHEMHH QIRTSIGVLM FITVPASIGI MALAQPLFTV FYGYDPIVLG HDPNHDGSRL LFYYAPVAIL ISLL SVTAS MLQGIDKQKL TVYVILASVV IKLALNYPLI MLFHTPGAIL STSIALLFAI GCNFYILKKY AKFKFSYSWI HFAKI FLYS FIMMLGVELV FFLANLFLEP TKLGYLIIII LGVTVGILIY GTITIKTRLA DEFLGEIPEK LRRRVRFLR

UniProtKB: Polysaccharide biosynthesis protein, putative

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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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 103967
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:

6-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-11ya:
Staphylococcus aureus MurJ R176A mutant

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