9IA5 | pdb_00009ia5

LpDEM from Escherichia coli


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Structural basis of lipopolysaccharide assembly by the outer membrane translocon holo-complex.

Chen, H.Siroy, A.Morales, V.Gurvic, D.Quentin, Y.Balor, S.Abuta'a, Y.A.Marteau, M.Froment, C.Caumont-Sarcos, A.Marcoux, J.Stansfeld, P.J.Fronzes, R.Ieva, R.

(2025) Nat Commun 16: 10404-10404

  • DOI: https://doi.org/10.1038/s41467-025-65370-2
  • Primary Citation Related Structures: 
    9I9Z, 9IA0, 9IA2, 9IA5

  • PubMed 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 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.


  • Organizational Affiliation
    • Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France.

Macromolecule Content 

  • Total Structure Weight: 119.43 kDa 
  • Atom Count: 7,203 
  • Modeled Residue Count: 891 
  • Deposited Residue Count: 1,052 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LPS-assembly protein LptD784Escherichia coliMutation(s): 0 
Gene Names: lptDimpostAyabGb0054JW0053
UniProt
Find proteins for P31554 (Escherichia coli (strain K12))
Explore P31554 
Go to UniProtKB:  P31554
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31554
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LPS-assembly lipoprotein LptE193Escherichia coliMutation(s): 0 
Gene Names: lptErlpBb0641JW0636
UniProt
Find proteins for P0ADC1 (Escherichia coli (strain K12))
Explore P0ADC1 
Go to UniProtKB:  P0ADC1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADC1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LPS-assembly lipoprotein LptMC [auth D]75Escherichia coliMutation(s): 0 
Gene Names: lptMyifLb4558JW3781
UniProt
Find proteins for P0ADN6 (Escherichia coli (strain K12))
Explore P0ADN6 
Go to UniProtKB:  P0ADN6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADN6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.63 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_4958

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--
Agence Nationale de la Recherche (ANR)FranceEnigma

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release