9DOO | pdb_00009doo

Cryo-EM structure of LptB2FG apo-III

  • Classification: LIPID TRANSPORT
  • Organism(s): Pseudomonas aeruginosa
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-09-19 Released: 2025-11-19 
  • Deposition Author(s): Su, C.C.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9DOO

This is version 1.1 of the entry. See complete history

Literature

Structural snapshots of Pseudomonas aeruginosa LptB 2 FG and LptB 2 FGC reveal insights into lipopolysaccharide recognition and transport.

Fiorentino, F.Cervoni, M.Wang, Y.Urner, L.H.Sauer, J.B.Tran, A.Corey, R.A.Rotili, D.Mai, A.Stansfeld, P.J.Imperi, F.Yu, E.W.Su, C.C.Robinson, C.V.Bolla, J.R.

(2025) Nat Commun 16: 11384-11384

  • DOI: https://doi.org/10.1038/s41467-025-66182-0
  • Primary Citation Related Structures: 
    9DOH, 9DOK, 9DOO, 9DOQ, 9DOR

  • PubMed Abstract: 

    Gram-negative bacteria are intrinsically resistant to many antibiotics because of densely packed lipopolysaccharides (LPS) in the outer leaflet of their outer membrane (OM), which acts as a highly effective barrier towards the spontaneous permeation of toxic molecules, including antibiotics. LPS are extracted from the inner membrane by the ABC transporter LptB 2 FGC and translocated across the periplasm via a protein bridge to the OM. While structural studies have elucidated aspects of Lpt function in enterobacteria, little is known about how this system operates in divergent species such as Pseudomonas aeruginosa, a major human pathogen. Here, we report five cryo-electron microscopy structures of P. aeruginosa LptB 2 FG and LptB 2 FGC, revealing a rigid body movement in the periplasmic β-jellyroll domains necessary for LPS to shuttle through the periplasmic space. Notably, these structures exhibit a significantly smaller LPS binding cavity compared to previously determined models, suggesting the ligand-unbound states of the transporter. Mass spectrometry and molecular dynamics simulations indicate that the phosphate groups of LPS are the key determinants for binding and that the transporter can also accommodate cardiolipin. Together, these findings reveal previously unappreciated structural diversity in the Lpt system and provide mechanistic insight into how pathogenic Gram-negative bacteria tailor LPS recognition and transport. This understanding offers new avenues for the development of novel inhibitors targeting membrane biogenesis.


  • Organizational Affiliation
    • Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.

Macromolecule Content 

  • Total Structure Weight: 139.82 kDa 
  • Atom Count: 9,363 
  • Modeled Residue Count: 1,186 
  • Deposited Residue Count: 1,237 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system ATP-binding protein LptBA [auth B],
B [auth A]
252Pseudomonas aeruginosaMutation(s): 0 
Gene Names: lptB_3lptBlptB_2CAZ10_21010GNQ48_11505GUL26_13595IPC1295_15315IPC737_20870NCTC13621_04169PAERUG_P19_London_7_VIM_2_05_10_06438
UniProt
Find proteins for A0A071L2Z5 (Pseudomonas aeruginosa)
Explore A0A071L2Z5 
Go to UniProtKB:  A0A071L2Z5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A071L2Z5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PermeaseC [auth G]358Pseudomonas aeruginosaMutation(s): 0 
Gene Names: lptGCAZ10_29115GNQ48_26920IPC737_18645NCTC13621_00519
UniProt
Find proteins for A0A071LDY1 (Pseudomonas aeruginosa)
Explore A0A071LDY1 
Go to UniProtKB:  A0A071LDY1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A071LDY1
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system permease protein LptFD [auth F]375Pseudomonas aeruginosaMutation(s): 0 
Gene Names: lptFCAZ10_29120DT376_04500GNQ48_26915GUL26_00985IPC1295_13765IPC737_18640PAERUG_P19_London_7_VIM_2_05_10_06506
UniProt
Find proteins for A0A071L107 (Pseudomonas aeruginosa)
Explore A0A071L107 
Go to UniProtKB:  A0A071L107
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A071L107
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-11-19 
  • Deposition Author(s): Su, C.C.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-12-31
    Changes: Data collection, Database references