9FDQ
Single particle cryo-EM structure of the AcrB V612F monomer in the O state
Summary for 9FDQ
| Entry DOI | 10.2210/pdb9fdq/pdb |
| EMDB information | 50332 |
| Descriptor | Multidrug efflux pump subunit AcrB (1 entity in total) |
| Functional Keywords | drug efflux, rnd transporter, transport protein |
| Biological source | Escherichia coli K-12 |
| Total number of polymer chains | 1 |
| Total formula weight | 114784.34 |
| Authors | Lazarova, M.,Frangakis, A.,Pos, K.M. (deposition date: 2024-05-17, release date: 2025-05-28, Last modification date: 2025-12-10) |
| Primary citation | Lazarova, M.,Eicher, T.,Bornsen, C.,Zeng, H.,Athar, M.,Okada, U.,Yamashita, E.,Spannaus, I.M.,Borgosch, M.,Cha, H.J.,Vargiu, A.V.,Murakami, S.,Diederichs, K.,Frangakis, A.S.,Pos, K.M. Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity. Nat Commun, 2025 Cited by PubMed Abstract: Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of cell envelope spanning systems and provide resistance to diverse antibiotics. Here, we identify two phylogenetic clusters of RND proteins with conserved binding pocket residues and show that the transfer of a single conserved residue between both clusters affects the resistance phenotype not only due to changes in the physicochemical properties of the binding pocket, but also due to an altered equilibrium between the conformational states of the transport cycle. We demonstrate, using single-particle cryo-electron microscopy, that AcrB and OqxB, which represent both clusters, adopt fundamentally different apo states, implying distinct mechanisms for initial substrate binding. The observed conformational plasticity appears phylogenetically conserved and likely plays a role in the diversification of the resistance phenotype among homologous RND pumps. PubMed: 41298458DOI: 10.1038/s41467-025-66751-3 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.47 Å) |
Structure validation
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