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- EMDB-52777: LpDE from Escherichia coli -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-52777
TitleLpDE from Escherichia coli
Map data
Sample
  • Complex: Lipopolysaccharide transport complex LptDE stabilized by the accessory protein YedD.
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: LPS-assembly lipoprotein LptE
KeywordsLipopolysaccharide transport / TRANSPORT PROTEIN
Function / homology
Function and homology information


transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / lipopolysaccharide binding
Similarity search - Function
LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsSiroy R / Fronzes R / Ieva R
Funding support France, 2 items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Agence Nationale de la Recherche (ANR)Enigma France
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of lipopolysaccharide assembly by the outer membrane translocon holo-complex.
Authors: Haoxiang Chen / Axel Siroy / Violette Morales / Dominik Gurvič / Yves Quentin / Stephanie Balor / Yassin A Abuta'a / Maurine Marteau / Carine Froment / Anne Caumont-Sarcos / Julien Marcoux ...Authors: Haoxiang Chen / Axel Siroy / Violette Morales / Dominik Gurvič / Yves Quentin / Stephanie Balor / Yassin A Abuta'a / Maurine Marteau / Carine Froment / Anne Caumont-Sarcos / Julien Marcoux / Phillip J Stansfeld / Rémi Fronzes / Raffaele Ieva /
Abstract: Lipopolysaccharide (LPS) assembly at the surfaces-exposed leaflet of the bacterial outer membrane (OM) is mediated by the OM LPS translocon. An essential transmembrane β-barrel protein, LptD, and a ...Lipopolysaccharide (LPS) assembly at the surfaces-exposed leaflet of the bacterial outer membrane (OM) is mediated by the OM LPS translocon. An essential transmembrane β-barrel protein, LptD, and a cognate lipoprotein, LptE, translocate LPS selectively into the OM external leaflet via a poorly understood mechanism. Here, we characterize two additional translocon subunits, the lipoproteins LptM and LptY (formerly YedD). We use single-particle cryo-EM analysis, functional assays and molecular dynamics simulations to visualize the roles of LptM and LptY at the translocon holo-complex LptDEMY, uncovering their impact on LptD conformational dynamics. Whereas LptY binds and stabilizes the periplasmic LptD β-taco domain that functions as LPS receptor, LptM intercalates the lateral gate of the β-barrel domain, promoting its opening and access by LPS. Remarkably, we demonstrate a conformational switch of the LptD β-taco/β-barrel interface alternating between contracted and extended states. β-strand 1 of LptD, which defines the mobile side of the lateral gate, binds LPS and performs a stroke movement toward the external leaflet during the contracted-to-extended state transition. Our findings support a detailed mechanistic framework explaining the selective transport of LPS to the membrane external leaflet.
History
DepositionFeb 7, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52777.png

Downloads & links

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Map

FileDownload / File: emd_52777.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.73 Å/pix.
x 360 pix.
= 263.16 Å		0.73 Å/pix.
x 360 pix.
= 263.16 Å		0.73 Å/pix.
x 360 pix.
= 263.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.6
Minimum - Maximum-32.548732999999999 - 41.112327999999998
Average (Standard dev.)-0.000000000009522 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 263.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52777_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52777_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lipopolysaccharide transport complex LptDE stabilized by the acce...

EntireName: Lipopolysaccharide transport complex LptDE stabilized by the accessory protein YedD.
Components
  • Complex: Lipopolysaccharide transport complex LptDE stabilized by the accessory protein YedD.
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: LPS-assembly lipoprotein LptE

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Supramolecule #1: Lipopolysaccharide transport complex LptDE stabilized by the acce...

SupramoleculeName: Lipopolysaccharide transport complex LptDE stabilized by the accessory protein YedD.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Co-purification of the third component YedD, identified in th sample by mass spectrometry analysis. An alphafold2-generated model of YedD can be rigid-body fitted in the low resolution density of the map.
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: LPS-assembly protein LptD

MacromoleculeName: LPS-assembly protein LptD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 89.754719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQL HQKEAPGQPE PVRTVDALGN VHYDDNQVIL KGPKGWANLN TKDTNVWEGD YQMVGRQGRG KADLMKQRGE N RYTILDNG ...String:
MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQL HQKEAPGQPE PVRTVDALGN VHYDDNQVIL KGPKGWANLN TKDTNVWEGD YQMVGRQGRG KADLMKQRGE N RYTILDNG SFTSCLPGSD TWSVVGSEII HDREEQVAEI WNARFKVGPV PIFYSPYLQL PVGDKRRSGF LIPNAKYTTT NY FEFYLPY YWNIAPNMDA TITPHYMHRR GNIMWENEFR YLSQAGAGLM ELDYLPSDKV YEDEHPNDDS SRRWLFYWNH SGV MDQVWR FNVDYTKVSD PSYFNDFDNK YGSSTDGYAT QKFSVGYAVQ NFNATVSTKQ FQVFSEQNTS SYSAEPQLDV NYYQ NDVGP FDTRIYGQAV HFVNTRDDMP EATRVHLEPT INLPLSNNWG SINTEAKLLA THYQQTNLDW YNSRNTTKLD ESVNR VMPQ FKVDGKMVFE RDMEMLAPGY TQTLEPRAQY LYVPYRDQSD IYNYDSSLLQ SDYSGLFRDR TYGGLDRIAS ANQVTT GVT SRIYDDAAVE RFNISVGQIY YFTESRTGDD NITWENDDKT GSLVWAGDTY WRISERWGLR GGIQYDTRLD NVATSNS SI EYRRDEDRLV QLNYRYASPE YIQATLPKYY STAEQYKNGI SQVGAVASWP IADRWSIVGA YYYDTNANKQ ADSMLGVQ Y SSCCYAIRVG YERKLNGWDN DKQHAVYDNA IGFNIELRGL SSNYGLGTQE MLRSNILPYQ NTL

UniProtKB: LPS-assembly protein LptD

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Macromolecule #2: LPS-assembly lipoprotein LptE

MacromoleculeName: LPS-assembly lipoprotein LptE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 22.486703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR ...String:
MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR SDEEQTSTTT DTPATPARVS TTLGNHHHHH HHH

UniProtKB: LPS-assembly lipoprotein LptE

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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

Concentration0.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris-HCl
50.0 mMNaClsodium chloride
0.03 %C24H46O11n-dodecyl-beta-D-maltoside
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107410
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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