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 9QGY | pdb_00009qgy

Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9QGY

This is version 1.1 of the entry. See complete history. 

Literature

A lipoprotein partner for the Escherichia coli outer membrane protein TolC.

Horne, J., Kaplan, E., Jin, B., Abbott, K., Flores, V., Petsolari, E., Gradon, J., Ntsogo, Y., Harris, A., Yu, D., Zarkan, A., Luisi, B.F.

(2026) Elife 15

  • DOI: https://doi.org/10.7554/eLife.110666
  • Primary Citation Related Structures: 
    9QGY, 9TG4

  • PubMed Abstract: 

    The outer membrane protein TolC from Escherichia coli belongs to an extensive superfamily whose members are found throughout the didermal, Gram-negative bacterial lineages. The protein serves as an activated exit duct in multi-drug efflux pumps and protein secretion machinery. Many TolC homologues bear a lipid modification on the N-terminus that embeds into the inner leaflet of the outer membrane and appears to have been a conserved feature; however, the moiety is absent entirely in the E. coli TolC. We have discovered that the E. coli lipoprotein YbjP interacts extensively with the periplasmic surface of TolC and its N-terminal lipid moiety is embedded in the membrane, mimicking the intramolecular and modification-membrane interactions seen in TolC homologues. Here, we present cryo-EM structures of the MacA-MacB-TolC and AcrA-AcrB-TolC tripartite pumps complexed to YbjP. Although the association occurs spontaneously both in vitro and in vivo, the YbjP-TolC interaction is not required for efflux activity under standard laboratory conditions. YbjP may contribute to stabilising the orientation and distribution of TolC in the outer membrane, as well as the expression of transporters for tryptophan and cyclic peptide toxins.


  • Organizational Affiliation: 
    • Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 498.06 kDa 
  • Atom Count: 32,502 
  • Modeled Residue Count: 4,198 
  • Deposited Residue Count: 4,516 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein TolC
A, B, C
471Escherichia coliMutation(s): 0 
Gene Names: tolC, colE1-i, mtcB, mukA, refI, toc, weeA, b3035, JW5503
UniProt
Find proteins for P02930 (Escherichia coli (strain K12))
Explore P02930 
Go to UniProtKB:  P02930
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02930
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized lipoprotein YbjP
D, E, F
153Escherichia coliMutation(s): 0 
Gene Names: ybjP, b0865, JW0849
UniProt
Find proteins for P75818 (Escherichia coli (strain K12))
Explore P75818 
Go to UniProtKB:  P75818
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75818
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Macrolide export protein MacA
G, H, I, J, K
G, H, I, J, K, L
371Escherichia coliMutation(s): 0 
Gene Names: macA, ybjY, b0878, JW0862
UniProt
Find proteins for P75830 (Escherichia coli (strain K12))
Explore P75830 
Go to UniProtKB:  P75830
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75830
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Macrolide export ATP-binding/permease protein MacB
M, N
209Escherichia coliMutation(s): 0 
Gene Names: macB, ybjZ, b0879, JW0863
EC: 7.6.2
UniProt
Find proteins for P75831 (Escherichia coli (strain K12))
Explore P75831 
Go to UniProtKB:  P75831
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75831
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom222451/Z/21/Z
European Research Council (ERC)European Union742210

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release
  • Version 1.1: 2026-10-07
    Changes: Data collection, Database references