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TitleAssembly and inhibition of transferable TMexCD1-TOprJ1 efflux pump.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 10025, Year 2025
Publish dateNov 14, 2025
AuthorsYu Shi / Mengyuan Li / Tao Cui / Jianhua Gan / Haomin Huang / Zhi Su / Runshi Yang / Xing Zhang / Huimin Zhang / Yu Feng / Youjun Feng /
PubMed AbstractRecent emergence and dissemination of plasmid-borne tmexCD1-toprJ1 tigecycline resistance threatens the efficacy of tigecycline as a "last-resort" defense against bacterial infections. Here, we ...Recent emergence and dissemination of plasmid-borne tmexCD1-toprJ1 tigecycline resistance threatens the efficacy of tigecycline as a "last-resort" defense against bacterial infections. Here, we report two cryo-EM structures of TMexCD1-TOprJ1 alone and in complex with its NMP inhibitor, and both are determined at the resolutions of 2.97 Å and 3.0 Å, respectively. The symmetry of overall architecture explains how the tripartite organization adopts a 3:6:3 protomer stoichiometry (TOprJ1: TMexC1: TMexD1) to assemble an elongated, rod-like pump spanning bacterial double membranes. The periplasmic TMexC1 adaptor bind the trimeric TOprJ1 funnel via a universal "tip-to-tip" contact, and bridges the bottom TMexD1 engine by extensive interactions. A unique form of resting (R) states is observed for TMexD1 trimer. Besides two binding-interfaces of TMexC1 with TOprJ1 and TMexD1, we characterize a substrate/inhibitor-loading cavity. Collectively, these findings constitute molecular bases for assembly and inhibition of transferable TMexCD1-TOprJ1 machinery, and benefit developing next-generation of antimicrobials targeting functional efflux pump.
External linksNat Commun / PubMed:41238543 / PubMed Central
MethodsEM (single particle)
Resolution2.97 - 3.0 Å
Structure data

61114

9j3d

EMDB-61114, PDB-9j3d:
Cryo-EM structure of TMexCD1-TOprJ1
Method: EM (single particle) / Resolution: 2.97 Å

61115

9j3e

EMDB-61115, PDB-9j3e:
Cryo-EM structure of TMexCD1-TOprJ1 in complex with 1-(1-naphthylmethyl)piperazine
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

PDB-1ean:
THE RUNX1 Runt domain at 1.70A resolution: A structural switch and specifically bound chloride ions modulate DNA binding

Source
  • klebsiella pneumoniae (bacteria)
KeywordsTRANSPORT PROTEIN / efflux pump / transporter / antibiotics / antimicrobial resistance

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