1. Department of Cell Membrane Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
2. Faculty of Pharmaceutical Science, 1-6 Yamada-oka, Osaka University, Suita, Osaka 565-0871, Japan
3. Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita 565-0871, Japan
4. CREST, Japan Science and Technology Corporation, Osaka 567-0047, Japan

Correspondence to: Akihito Yamaguchi^1,2,4 Correspondence and requests for materials should be addressed to A. Y. (e-mail: Email: akihito@sanken.osaka-u.ac.jp). Coordinates have been deposited with the Protein Data Bank under accession code 1IWG.

Abstract

AcrB is a major multidrug exporter in Escherichia coli. It cooperates with a membrane fusion protein, AcrA, and an outer membrane channel, TolC. We have determined the crystal structure of AcrB at 3.5 Å resolution. Three AcrB protomers are organized as a homotrimer in the shape of a jellyfish. Each protomer is composed of a transmembrane region 50 Å thick and a 70 Å protruding headpiece. The top of the headpiece opens like a funnel, where TolC might directly dock into AcrB. A pore formed by three -helices connects the funnel with a central cavity located at the bottom of the headpiece. The cavity has three vestibules at the side of the headpiece which lead into the periplasm. In the transmembrane region, each protomer has twelve transmembrane -helices. The structure implies that substrates translocated from the cell interior through the transmembrane region and from the periplasm through the vestibules are collected in the central cavity and then actively transported through the pore into the TolC tunnel.