Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 11649, Year 2025
Publish date	Nov 26, 2025
Authors	Mariya Lazarova / Thomas Eicher / Clara Börnsen / Hui Zeng / Mohd Athar / Ui Okada / Eiki Yamashita / Inga M Spannaus / Max Borgosch / Hi-Jea Cha / Attilio V Vargiu / Satoshi Murakami / Kay Diederichs / Achilleas S Frangakis / Klaas M Pos /
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 ...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.
External links	Nat Commun / PubMed:41298458 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.89 - 3.9 Å
Structure data	EMDB-50328: Single particle cryo-EM maps of AcrB wildtype monomer classes in DDM Method: EM (single particle) / Resolution: 3.6 Å EMDB-50329: Single particle cryo-EM maps of AcrB V612F monomer classes in DDM Method: EM (single particle) / Resolution: 3.9 Å 50331 9fdp EMDB-50331: Single particle cryo-EM maps of AcrB V612W monomer classes in DDM PDB-9fdp: Single particle cryo-EM structure of the AcrB V612W monomer in the O state Method: EM (single particle) / Resolution: 3.3 Å 50332 9fdq EMDB-50332: Single particle cryo-EM maps of AcrB V612F monomer classes in salipro nanodiscs PDB-9fdq: Single particle cryo-EM structure of the AcrB V612F monomer in the O state Method: EM (single particle) / Resolution: 3.47 Å 50334 9fdz EMDB-50334, PDB-9fdz: Single particle cryo-EM structure of the multidrug efflux pump OqxB from Klebsiella pneumoniae Method: EM (single particle) / Resolution: 2.86 Å EMDB-50335: Single particle cryo-EM maps of OqxB monomer classes in salipro nanodiscs Method: EM (single particle) / Resolution: 3.59 Å EMDB-50645: Single particle cryo-EM maps of AcrB wildtype monomers reconstituted in salipro nanodiscs Method: EM (single particle) / Resolution: 2.9 Å PDB-8zxs: Crystal structure of multidrug efflux transporter OqxB from Klebsiella pneumoniae Method: X-RAY DIFFRACTION / Resolution: 2.75 Å PDB-9fe2: Crystallographic structure of AcrB V612W with bound minocycline Method: X-RAY DIFFRACTION / Resolution: 1.89 Å PDB-9fe3: Crystallographic structure of AcrB V612W Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-9fe4: Crystallographic structure of AcrB V612F Method: X-RAY DIFFRACTION / Resolution: 2.8 Å PDB-9fhc: Crystallographic structure of AcrB V612F with bound minocycline Method: X-RAY DIFFRACTION / Resolution: 2.2 Å PDB-9fhg: Crystallographic structure of AcrB V612N in LTO state Method: X-RAY DIFFRACTION / Resolution: 3 Å PDB-9fhj: Crystallographic structure of AcrB V612N in TTT state Method: X-RAY DIFFRACTION / Resolution: 3.55 Å
Chemicals	ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergentYM ChemComp-GOL: GLYCEROL ChemComp-HOH: WATER ChemComp-MIY: (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- / medication, antibioticYM
Source	escherichia coli k-12 (bacteria) klebsiella pneumoniae (bacteria) synthetic construct (others)
Keywords	MEMBRANE PROTEIN / Multidrug efflux transporter / Membrane transporter / Antimicrobial resistance / AMR / Klebsiella pneumoniae / TRANSPORT PROTEIN / Drug efflux / RND transporter