9RLK | pdb_00009rlk

LolCDE(delta 235-252) complex with Pal lipoprotein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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

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This is version 1.1 of the entry. See complete history

Literature

Liganded LolCDE structures reveal a common substrate-LolE interaction guiding bacterial lipoprotein transport.

Szewczyk, P.Greene, N.P.Symmons, M.F.Hardwick, S.W.Koronakis, V.

(2026) Proc Natl Acad Sci U S A 123: e2520579123-e2520579123

  • DOI: https://doi.org/10.1073/pnas.2520579123
  • Primary Citation Related Structures: 
    9RLC, 9RLD, 9RLE, 9RLF, 9RLG, 9RLH, 9RLI, 9RLJ, 9RLK

  • PubMed Abstract: 

    Bacterial lipoproteins are key structural components of the outer membrane in Gram-negative bacteria and vital components of machineries required for its biosynthesis and maintenance. The Lol system, essential for viability, directs transport of lipoproteins from the site of biosynthesis on the inner membrane to the outer membrane and has been the target of extensive efforts to develop novel antimicrobial drugs. In the first stage of this transport process, newly synthesized lipoproteins are released from the inner membrane by the ABC transporter LolCDE and passed to the periplasmic chaperone, LolA. Here, we show cryo-EM structures of LolCDE in complex with three different lipoprotein substrates, Lpp, Pal, and LolB, with the latter two bearing a disordered peptide linker between the acyl chains and the globular domain. Our work reveals that when the mature lipoprotein lacks an unstructured linker, the N-terminal portion of the protein is in an unfolded state for transport. The lipoproteins make a sequence-independent but structurally conserved interaction with a cleft on the surface of the periplasmic domain of LolE that promotes efficient transport. We propose a model of lipoprotein export where this interaction acts as pivot point for the peptide portion of the lipoprotein allowing the acyl chains to rotate 180° from their initial position in LolCDE to their binding site in LolA. Our results demonstrate how LolCDE can extrude lipoproteins of diverse sequence and structure and reveal an important detail of a transport process fundamental to bacterial physiology.


  • Organizational Affiliation
    • Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 158.31 kDa 
  • Atom Count: 9,647 
  • Modeled Residue Count: 1,255 
  • Deposited Residue Count: 1,441 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipoprotein-releasing system transmembrane protein LolCA [auth C]399Escherichia coli K-12Mutation(s): 0 
Gene Names: lolCycfUb1116JW5161
UniProt
Find proteins for P0ADC3 (Escherichia coli (strain K12))
Explore P0ADC3 
Go to UniProtKB:  P0ADC3
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UniProt GroupP0ADC3
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipoprotein-releasing system transmembrane protein LolEB [auth E]398Escherichia coli K-12Mutation(s): 0 
Gene Names: lolEycfWb1118JW1104
UniProt
Find proteins for P75958 (Escherichia coli (strain K12))
Explore P75958 
Go to UniProtKB:  P75958
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UniProt GroupP75958
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipoprotein-releasing system ATP-binding protein LolDC [auth D],
D [auth F]
241Escherichia coli K-12Mutation(s): 0 
Gene Names: lolDycfVb1117JW5162
EC: 7.6.2
UniProt
Find proteins for P75957 (Escherichia coli (strain K12))
Explore P75957 
Go to UniProtKB:  P75957
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UniProt GroupP75957
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidoglycan-associated lipoproteinE [auth P]162Escherichia coli K-12Mutation(s): 0 
Gene Names: palexcCb0741JW0731
UniProt
Find proteins for P0A912 (Escherichia coli (strain K12))
Explore P0A912 
Go to UniProtKB:  P0A912
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UniProt GroupP0A912
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONWarp

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/V000616/1

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release
  • Version 1.1: 2026-02-04
    Changes: Data collection, Database references