Structure

AcrB is a homotrimer composed of 3 protomers, each 1049 residues in length. The protomers are arranged such that a 3-fold symmetrical axis exists which is perpendicular to the membrane plane. Each unit consists of:

1. A transmembrane region (50Å thick, 80Å wide); located in the inner membrane
2. An extracellular domain/ headpiece (70Å thick, 100Å wide); located in the periplasm

Fig1 - A Pymol generated diagram of AcrB showing its domains

Transmembrane domain

Location: Inner membrane

Protomeric composition: 12 alpha helices

• 3 protomeric transmembrane domains arranged in a ring-like manner with a central hole
• Hole of diameter 30Å extends across the inner membrane and connects to bottom of headpiece
• 3 transmembrane domains associate loosely with each other; contrast to the strong interactions that exist within the headpiece

Extracellular Domain/ Headpiece

Location: Periplasm

Protomeric composition: 6 subunits (PN1, PN2, PC1, PC2, DN, DC)

• Top section: DN and DC 
• Docking site for TolC (Evidence: Internal diameter of funnel-like opening = Diameter of TolC conduit = 30Å)
• Long hairpin structure ~35Å protrudes from each protomer and inserts into that of the next protomer; creates an interlocking arrangement that provides a very strong interaction holding the headpiece together 
• Middle section: PN1, PN2, PC1, PC2 (Pore domain)
• Contains binding sites for drugs
• Bottom section: Central cavity (Connects to transmembrane region)

Pore domain

Location: Middle section of headpiece (Connects funnel-like top and central cavity)

Protomeric composition: PN1, PN2, PC1 and PC2 domains

• Arrangement of domains (clockwise as viewed from top): PN1 inside the headpiece, PN2, PC1 and PC2 outside
• Each domain contains a characteristic structural motif: 2 (directly repeated) β strand-α helix- β strand motifs sandwiched with each other
• Pore is formed by 3 α helices, one contributed per PN1 domain
• In the access monomer, high MW drugs binds to the proximal site located between the  β sheets of PC1 and PC2*
• Phenylalanine loop located between the C β2' and C β3' chains of PC1; loops plays an important role in the transport mechanism*
• Vestibules at the side of the headpiece are present between PN2 of one protomer and PC2 of the next and surround the cavity*

*Further details on structure and binding of drugs within this domain will be provided under the subtopic 'Rifampicin-bound AcrB' in Functional Mechanism. Contributions of specific structural elements and sites will also be elaborated on.

Fig. 2 - Model of AcrB (associated with AcrA and TolC) illustrating a. features contained in the headpiece and  b. the proposed transport mechanism.

Proposed Transport Mechanisms- An Overview

Substrates must first gain access to central cavity in headpiece before they are transported through the pore and funnel-like domains. After passing from the bottom to the top of the headpiece, they finally exit through TolC.

1. Substrates located on membrane plane or in outer leaflet of inner membrane

• Gain access to cavity via vestibules

2. Substrates located in cytoplasm or inner leaflet of inner membrane

• Access to cavity might involve transmembranal grooves that span the inner membrane
• Location of grooves aligned between PC1 and PC2
• Top of grooves connected to cavity which implicates a possible pathway for substrates across inner membrane

Drugs are exported via a functionally rotating mechanism which involves each protomer undergoing conformational changes to assume 3 different states. The presence of proximal and distal binding sites are also key. Whether the drugs can bind and/or exit depends on the individual forms adopted by each protomer. More details on the transport mechanism and binding sites of AcrB are under 'Functional Mechanism'.