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- PDB-9ia2: LpDEM from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9ia2
TitleLpDEM from Escherichia coli
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly lipoprotein LptM
  • LPS-assembly protein LptD
KeywordsTRANSPORT PROTEIN / Lipopolysaccharide transport
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
Prokaryotic lipoprotein-attachment site / LPS-assembly lipoprotein LptM, conserved region / 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 lipoprotein LptM / LPS-assembly protein LptD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsSiroy, R. / Fronzes, R. / Ieva, R.
Funding support France, 2items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
C: LPS-assembly lipoprotein LptM


Theoretical massNumber of molelcules
Total (without water)119,4263
Polymers119,4263
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein LPS-assembly protein LptD / Organic solvent tolerance protein


Mass: 89754.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptD, imp, ostA, yabG, b0054, JW0053 / Production host: Escherichia coli (E. coli) / References: UniProt: P31554
#2: Protein LPS-assembly lipoprotein LptE / Rare lipoprotein B


Mass: 21381.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptE, rlpB, b0641, JW0636 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADC1
#3: Protein LPS-assembly lipoprotein LptM / LptD oxidative maturation-associated lipoprotein


Mass: 8289.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptM, yifL, b4558, JW3781 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADN6
Has protein modificationY

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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

ComponentName: Lipopolysaccharide transport complex LptDEM. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HClC4H11NO31
250 mMsodium chlorideNaCl1
30.03 %n-dodecyl-beta-D-maltosideC24H46O111
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21rc1_4958model refinement
3EPUimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198109 / Algorithm: FOURIER SPACE / Symmetry type: POINT
RefinementCross valid method: NONE

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