9FZ5 | pdb_00009fz5

Cryo-EM structure of LptDE-YedD complex from Escherichia Coli


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Optimal functioning of the Lpt bridge depends on a ternary complex between the lipocalin YedD and the LptDE translocon.

Gennaris, A.Nguyen, V.S.Thouvenel, L.Csoma, N.Vertommen, D.Iorga, B.I.Remaut, H.Collet, J.F.

(2025) Cell Rep 44: 115446-115446

  • DOI: https://doi.org/10.1016/j.celrep.2025.115446
  • Primary Citation of Related Structures:  
    9FZ5

  • PubMed Abstract: 

    The outer membrane is an efficient permeability barrier that protects gram-negative bacteria against external assaults, including many antibiotics. The unique permeability features of the outer membrane are due to the presence of lipopolysaccharide (LPS) molecules in its outer leaflet. LPS transport relies on the essential lipopolysaccharide transport (Lpt) pathway, which forms a bridge from the inner to the outer membrane. The LptDE translocon inserts LPS into the outer leaflet. Here, we identify the lipocalin YedD as a component of the translocon. Cryoelectron microscopy of the YedD-LptDE complex reveals that YedD binds LptD at a critical interface between its β-barrel and periplasmic β-taco domain. The YedD-LptDE complex is functionally relevant: under conditions where the connectivity of the β-taco and Lpt bridge is compromised, the absence of YedD decreases cell viability and causes LPS accumulation in the inner membrane. Our findings establish YedD as an Lpt component required for optimal LPS transport.


  • Organizational Affiliation

    WELBIO Department, WEL Research Institute, Avenue Pasteur, 6, 1300 Wavre, Belgium; de Duve Institute, Université catholique de Louvain (UCLouvain), Avenue Hippocrate 75, 1200 Brussels, Belgium. Electronic address: alexandra.gennaris@uclouvain.be.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LPS-assembly protein LptD759Escherichia coli K-12Mutation(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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LPS-assembly lipoprotein LptE149Escherichia coli K-12Mutation(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:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized lipoprotein YedD117Escherichia coli K-12Mutation(s): 0 
Gene Names: yedDb1928JW1913
UniProt
Find proteins for P31063 (Escherichia coli (strain K12))
Explore P31063 
Go to UniProtKB:  P31063
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31063
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fonds de la Recherche Scientifique (FNRS)BelgiumWELBIO-CR-2015A-03
Fonds de la Recherche Scientifique (FNRS)BelgiumWELBIO-CR-2019C-03
Research Foundation - Flanders (FWO)BelgiumG0H5916N
Research Foundation - Flanders (FWO)Belgium12ZM421N

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release