9LYQ

Structure of RND efflux pump MdtB

Summary for 9LYQ

• Entry DOI: 10.2210/pdb9lyq/pdb
• EMDB information: 63321
• Descriptor: Multidrug resistance protein MdtB (1 entity in total)
• Functional Keywords: membrane protein, e.coli., cryo-em, efflux pump., transport protein
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 3
• Total formula weight: 336461.46

Authors

Dutta, S.,Padmanaban, S.,Fernando, R.C. (deposition date: 2025-02-20, release date: 2025-12-10, Last modification date: 2026-01-21)

Primary citation

Padmanaban, S.,Rencilin, C.F.,Biswas, R.,Dutta, S.
Cryo-EM reveals the structural heterogeneity and conformational flexibility of multidrug efflux pumps MdtB and MdtF.
Mbio, :e0268425-e0268425, 2025

PubMed Abstract: Resistance-nodulation-cell division (RND) efflux pumps are the major cause of multidrug resistance in bacteria, particularly in Gram-negative bacteria. They are complex molecular machines forming tripartite assemblies that actively transport out a wide range of antimicrobial agents, including antibiotics, biocides, and host defense molecules. However, the presence of multiple RND transporters with overlapping functions in a single bacterium raises questions about their individual functional relevance. In this study, we determined the cryo-electron microscopy (cryo-EM) structures of two distinct hydrophobic and amphiphilic efflux (HAE)-RND transporters from MdtB and MdtF. MdtB transporter is a part of the two-RND subunit system MdtABC. MdtF is a unique class of RND transporter whose expression is regulated by oxygen availability and is crucial for the survival of in anaerobic growth conditions. The cryo-EM structures of MdtB and MdtF reveal a novel conformational state of HAE-RND efflux pumps. While the MdtB structure adopts an intermediate state, MdtF displays structural dynamics in the presence of n-dodecyl-β-D-maltoside (DDM). MdtF at 2.8 Å resolution displayed a significant conformational change in the transmembrane core helices and flexibility in the transmembrane domain. Our findings highlight the significance of the novel structural state during the substrate transport mechanism. Furthermore, our structural analysis provides insights into drug-binding sites and the transport mechanism of these important transporters.

PubMed: 41370088
DOI: 10.1128/mbio.02684-25

Experimental method

ELECTRON MICROSCOPY (3.9 Å)