How Cryo-EM Has Expanded Our Understanding of Membrane Transporters

Abstract

Over the past two decades, technological advances in membrane protein structural biology have provided insight into the molecular mechanisms that transporters use to move diverse substrates across the membrane. However, the plasticity of these proteins' ligand binding pockets, which allows them to bind a range of substrates, also poses a challenge for drug development. Here we highlight the structure, function, and transport mechanism of ATP-binding cassette/solute carrier transporters that are related to several diseases and multidrug resistance: ABCB1, ABCC1, ABCG2, SLC19A1, and SLC29A1. SIGNIFICANCE STATEMENT: ATP-binding cassette transporters and solute carriers play vital roles in clinical chemotherapeutic outcomes. This paper describes the current understanding of the structure of five pharmacologically relevant transporters and how they interact with their ligands.

Fig. 1.

Structures of transporters discussed in the review. TMs are shown in lighter shades while NBDs are colored in darker tones. PDB accession codes are as follows: ABCB1 (6FN4), ABCC1 (5UJ9), ABCG2 (6VXF), SLC19A1 (7XPZ), SLC29A1 (6OB6).

Fig. 2.

Top panel: Alternating access model of transporters used by ABCB1, ABCC1, and ABCG2. TMs are shown in lighter shades while NBDs are colored in darker tones. Substrate is denoted as a gray diamond and ATP molecules are denoted as yellow ovals. Bottom panel: Rocker-Switch model used by SLC19A1 and SLC29A1. Substrate is denoted as a gray diamond.

Fig. 3.

(A) Structure of ABCB1 (PDB: 6QEX). TMDs are shown in lighter shades while NBDs are shown in darker tones. Ligand binding site and access tunnel shown as gray spheres. Structure of human/mouse chimeric ABCB1 bound to Taxol, a substrate (B, PDB: 6QEX) and to Encequidar, an inhibitor (C, PDB: 7O9W). Ligands are shown as gray sticks. Substrate binding site is outlined in black dashed lines, while the inhibitor binding site is outlined in blue dashed lines. (D) Structure of human/mouse chimeric ABCB1 (PDB: 6QEX). TMDs are shown in lighter shades while NBDs are shown in darker tones. Cholesterol molecules shown in black spheres and phospholipids are shown in purple spheres. Bound Taxol molecule is not shown.

Fig. 4.

Structure of apo bABCC1 (A, PDB: 5UJ9) and ATP-bound, outward-facing bABCC1 (B, PDB: 6BHU). TMs are shown in lighter shades while NBDs are colored in darker tones. TMD0 is shown in gray and L0 is shown in black. Coupling helices are outlined in yellow boxes.

Fig. 5.

(A) Binding pocket of bABCC1 (PDB: 5UJA). P-pocket is shown in blue, H-pocket is shown in red. LTC₄ ligand is shown as sticks, with the hydrophilic portion colored in green and the hydrophobic lipid tail colored in black. (B) Alternate view of the P-pocket only bound to the hydrophilic portion of LTC₄. (C) Alternate view of the H-pocket only bound to the lipid tail of LTC₄.

Fig. 6.

Structures of ligand-bound ABCG2. Top panels show cut-away from the binding interface while bottom panels show the view up the binding cavity. Ligands are shown as gray sticks. One monomer is shown in a bright color (TMD) while the second is shown in a pastel shade (TMD’). Left panels: Estrone 3-sulfate-bound ABCG2 (cyan, PDB: 6HCO). Middle panels: MZ29-bound ABCG2 (green, PDB: 6ETI). Right panels: MB136-bound ABCG2 (magenta, PDB: 6FEQ).

Fig. 7.

Venn diagram of selected compounds reported to bind ABCB1, ABCC1, and/or ABCG2 to show the overlapped specificity for the ABC transporters (based on reported structures).

Fig. 8.

Residues of ABCG2 mapped onto the structure of ABCG2 (PDB: 6VXF) as gray spheres. C592 residue is shown as a white sphere to avoid confusion with C608.

Fig. 9.

Left panel: Structure of 5-MTHF-bound SLC19A1 (PDB: 8GOE). N-terminal domain is shown in green, C-terminal domain in purple. Residues important for binding are shown in bold. Middle panel: Cutaway of ligand binding site to remove C-terminal domain. Right panel: Cutaway of ligand binding site to remove N-terminal domain.

Fig. 10.

(A) Structure of SLC29A1 bound to Dilazep (PDB: 6OB7) and NBMPR (PDB: 6OB6). N-terminal domain is shown in orange, C-terminal domain is shown in hot pink, and ligands are shown as gray spheres. Dilazep occupies the orthosteric site and opportunistic site 1 (B) while NBMPR occupies the orthosteric site and opportunistic site 2 (C).