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- PDB-9kn3: Cryo-EM structure of LptDEM complex from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9kn3
TitleCryo-EM structure of LptDEM complex from Escherichia coli
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly protein LptD
  • Uncharacterized lipoprotein YifL
KeywordsMEMBRANE PROTEIN / LPS / Transporter / Complex
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 K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsTsukazaki, T. / Kohga, H. / Miyazaki, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Cell Rep / Year: 2025
Title: Structural basis of lipopolysaccharide translocon assembly mediated by the small lipoprotein LptM.
Authors: Ryoji Miyazaki / Mai Kimoto / Hidetaka Kohga / Tomoya Tsukazaki /
Abstract: Gram-negative bacteria possess an outer membrane (OM) that acts as a barrier against toxic compounds. Lipopolysaccharide (LPS) in the outer leaflet of the OM is crucial for barrier function and is ...Gram-negative bacteria possess an outer membrane (OM) that acts as a barrier against toxic compounds. Lipopolysaccharide (LPS) in the outer leaflet of the OM is crucial for barrier function and is transported to the OM by the LPS transport system. The LPS translocon (the LptDE complex), mediates LPS assembly into the OM. Recently, the small lipoprotein LptM was identified as an LptDE interactor that facilitates LptD maturation. However, its mechanism remains unclear. Here, we investigate the detailed interaction between LptM and LptD. We find that LptM interacts with the folded LptD intermediate at the late stage of its maturation. Mutational analyses demonstrate that the N-terminal conserved region of LptM is essential for its function. Cryoelectron microscopy structural analysis of the Escherichia coli LptDEM complex, combined with biochemical analyses, reveals the molecular basis of the LptM-LptD interaction and its functional importance. Thus, we propose that LptM stabilizes LptD for proper assembly.
History
DepositionNov 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,3563
Polymers113,3563
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 LPS-assembly protein LptD / Organic solvent tolerance protein


Mass: 87149.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / 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: 19479.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lptE, rlpB, b0641, JW0636 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADC1
#3: Protein Uncharacterized lipoprotein YifL


Mass: 6727.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: 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: LptDEM complex in Nanodisc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 4.648 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -1600 nm / Nominal defocus min: -600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 428907 / Symmetry type: POINT
Atomic model buildingB value: 108.5 / Protocol: AB INITIO MODEL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 72.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00927572
ELECTRON MICROSCOPYf_angle_d0.691810294
ELECTRON MICROSCOPYf_chiral_restr0.04991079
ELECTRON MICROSCOPYf_plane_restr0.00561365
ELECTRON MICROSCOPYf_dihedral_angle_d4.87711031

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