9V52

Structure of TolC and YbjP closed state complex

This is a non-PDB format compatible entry.

Summary for 9V52

• Entry DOI: 10.2210/pdb9v52/pdb
• EMDB information: 64784
• Descriptor: Outer membrane protein TolC, Uncharacterized lipoprotein YbjP (2 entities in total)
• Functional Keywords: multidrug efflux pump, tolc, ybjp, acra, acrb, lipoprotein, antibiotic resistance, gram-negative, protein transport
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 6
• Total formula weight: 218389.93

Authors

Ge, X.F.,Gu, Z.W.,Wang, J.W. (deposition date: 2025-05-25, release date: 2025-11-05, Last modification date: 2026-06-10)

Primary citation

Ge, X.,Gu, Z.,Wang, J.
Structural mechanisms of pump assembly and drug transport in the AcrAB-TolC efflux system.
Elife, 14:-, 2026

PubMed Abstract: Tripartite multidrug efflux pumps that span the cell envelope are essential for antibiotic resistance in Gram-negative bacteria. Here, we report cryo-EM structures of two endogenous efflux complexes from : a TolC-YbjP subcomplex at 3.56 Å resolution and the complete TolC-YbjP-AcrABZ pump at 3.39 Å. Structural analysis reveals that YbjP, a previously uncharacterized lipoprotein, binds TolC in a 3:3 stoichiometry, bridging the TolC protomers at their equatorial domain. Clear density of the mature YbjP's N-terminal Cys19 indicates that YbjP is anchored to the outer membrane by an N-terminal lipid moiety. Notably, YbjP remains bound as TolC undergoes AcrA-induced opening, suggesting that this accessory protein accommodates the conformational change. The AcrB trimer simultaneously presents three distinct conformational states (L, T, and O), capturing a complete transport cycle. These high-resolution structures provide insights into the architecture and mechanism of clinically relevant efflux machinery, identifying YbjP as a previously unrecognized structural component that contributes to TolC positioning, and may assist in its membrane localization.

PubMed: 42007677
DOI: 10.7554/eLife.109684

Experimental method

ELECTRON MICROSCOPY (3.56 Å)