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Structure of the human multidrug transporter ABCG2

Abstract

ABCG2 is a constitutively expressed ATP-binding cassette (ABC) transporter that protects many tissues against xenobiotic molecules. Its activity affects the pharmacokinetics of commonly used drugs and limits the delivery of therapeutics into tumour cells, thus contributing to multidrug resistance. Here we present the structure of human ABCG2 determined by cryo-electron microscopy, providing the first high-resolution insight into a human multidrug transporter. We visualize ABCG2 in complex with two antigen-binding fragments of the human-specific, inhibitory antibody 5D3 that recognizes extracellular loops of the transporter. We observe two cholesterol molecules bound in the multidrug-binding pocket that is located in a central, hydrophobic, inward-facing translocation pathway between the transmembrane domains. Combined with functional in vitro analyses, our results suggest a multidrug recognition and transport mechanism of ABCG2, rationalize disease-causing single nucleotide polymorphisms and the allosteric inhibition by the 5D3 antibody, and provide the structural basis of cholesterol recognition by other G-subfamily ABC transporters.

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Figure 1: Transport and ATPase activities of liposome-reconstituted ABCG2.
Figure 2: ABCG2 structure.
Figure 3: ABCG2–5D3(Fab) interaction.
Figure 4: Translocation pathway.
Figure 5: Proposed transport mechanism.

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Acknowledgements

This research was supported by the Swiss National Science Foundation through the National Centre of Competence in Research (NCCR) TransCure, and by a Swiss Federal Institute of Technology Zürich (ETH Zürich) research grant ETH-22-14-1. We thank the staff of the X06SA beamline of the Swiss Light Source for support during data collection. We thank K. Goldie, A. Fecteau-LeFebre, and R. McLeod for support during electron microscope use, and R. Adaixo, L. Muckenfuss, N. Biyani, and R. Righetto for support and discussions during EM data analysis. We thank L. Lancien and B. Prinz for help with protein expression and cell culture work. We thank B. Sorrentino for providing the 5D3-producing hybridoma cell line, B. Stieger for discussions about transport assays, and J.-I. Kim for initial ABCG2 expression and purification experiments.

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Authors and Affiliations

Authors

Contributions

I.M. expressed human and rat ABCG2. I.M. and S.M.J. purified and reconstituted ABCG2 in liposomes and nanodiscs. S.M.J. performed functional assays. J.K. performed initial negative-stain and cryo-EM analyses and prepared all grids. N.M.I.T. and H.S. performed cryo-EM data collection. N.M.I.T. performed ABCG2 structure determination and built the ABCG2 model. I.M., K.P.L. and N.M.I.T. revised the model, and N.M.I.T. performed model refinement. I.M. determined the 5D3-Fab crystal structure. K.P.L., I.M., S.M.J., and H.S. conceived the project and planned the experiments. I.M., S.M.J. and K.P.L. wrote the manuscript; all authors contributed to its revision.

Corresponding authors

Correspondence to Henning Stahlberg or Kaspar P. Locher.

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The authors declare no competing financial interests.

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Reviewer Information Nature thanks A. Ward and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Figure 1 Functional studies of liposome-reconstituted ABCG2.

a, Transport curves showing E1S uptake by ABCG2 in the presence and absence of ATP. b, The rate of E1S transport was measured at different E1S concentrations and the Michaelis constant was determined. c, ATP-dependent transport curves showing E1S uptake in the presence and absence of Ko143 or 5D3-Fab. d, The 30 s to 2 min linear portion of the curves from c used to determine the initial rates of E1S transport. e, Representative SDS–PAGE to determine the orientation of liposome-reconstituted YFP–3C–ABCG2 using in-gel fluorescence, comparing the intensity of free YFP after the addition of 3C protease in disrupted and non-disrupted samples; 54 ± 2% of ABCG2 was oriented with the NBDs on the outside of the proteoliposomes and all assays were subsequently corrected for this value; error, s.d. (n = 3). Non-disrupted supernatant (+3C) (lane 1); disrupted supernatant (+3C) (lane 2); non-disrupted supernatant (−3C) (lane 3); disrupted supernatant (−3C) (lane 4). f, The basal ATPase activity of nanodisc-reconstituted ABCG2 is equivalent to the E1S-stimulated activity of liposome-reconstituted ABCG2 and cannot be stimulated further. ABCG2 is not responsive to cholate in the presence or absence of E1S. The curves have been normalized to the basal ATPase activity of liposome-reconstituted ABCG2. In ad and f, two separate experiments were performed in triplicate (error bars, s.d.).

Extended Data Figure 2 Cryo-EM map generation and atomic model refinement.

a, An example micrograph (drift-corrected, dose-weighted, and low-pass filtered to 20 Å) of the nanodisc-reconstituted ABCG2–5D3(Fab) data set. White scale bar, 1,000 Å. b, Averages of the 28 most prevalent two-dimensional class averages of the final round of two-dimensional classification, sorted in decreasing order by the number of particles assigned to each class. c, Map obtained from the RELION three-dimensional auto-refine procedure shown at a lower (white, transparent) and higher (blue, non-transparent) threshold. Density corresponding to the nanodisc is indicated with an arrow. d, Same as c but rotated. e, Angular distribution plot for the final reconstruction. The refinement map is shown at two different thresholds as in c, in the same orientation. f, FSC from the RELION auto-refine procedure of the unmasked half-maps (yellow), the random-phase corrected half-maps (green), the half-maps after masking (blue), and the half-maps after masking and correction for the influence of the mask (red). A horizontal line (black) is drawn for the FSC = 0.143 criterion. For both the unmasked and the corrected FSC curves, their intersection with the FSC = 0.143 line is indicated by an arrow, and the resolution at this point is indicated. g, FSC of the final model versus the map calculated with all data after local-resolution filtering, against which it was refined, (dark blue) and of the final model with introduced shifts (up to 0.3 Å) refined against the first unfiltered half-map (half-map 1) versus the same unfiltered half-map (violet) and versus the other unfiltered half-map (half-map 2) against which it was not refined (grey).

Extended Data Figure 3 Local resolution.

a, Full view of the RELION local-resolution-filtered map coloured by local resolution as calculated by ResMap. b, Same as a but only showing the posterior half (front clipping plane in the middle of the molecule). c, Same as a but only showing a region up to 3 Å around one chain of ABCG2 (including the putative cholesterol molecule and side chains of the NBD). d, Same as c but rotated. e, Same as a but only showing a region up to 3 Å around one 5D3-Fab. f, Same as e but rotated.

Extended Data Figure 4 Fit of the model to the density.

a, Fit of fragments of the final model of the ABCG2 TMD to the post-processed and masked map from RELION. A region of up to 2 Å around the atoms is shown. The residue numbers are indicated, as are helices that are contained in these fragments and the EL3. b, Same as a but showing regions of 5D3-Fab. Residue numbers and whether the fragment belongs to the heavy or the light chain is indicated. c, Same as b but showing regions of the 5D3-Fab constant domain. d, Fit of the ABCG2 NBD model to the local-resolution-filtered map. A region of up to 3 Å around one ABCG2 NBD (including side chains) is shown. e, Same as a but showing the cholesterol (CHL) molecule. f, Fit of fragments of ABCG2 TM2, TM5a, and cholesterol to the post-processed and masked map from RELION. A region of up to 2 Å around the atoms is shown. g, Same as f but rotated by 180°.

Extended Data Figure 5 The X-ray structure and electrostatic surface potential of 5D3-Fab.

a, Cartoon representation of the X-ray structure of 5D3-Fab. The light and heavy chain CDR1s are coloured red, CDR2s are blue and CDR3s are purple. b, The molecular surface of 5D3-Fab, colour-coded by electrostatic potential ranging from blue (most positive) to red (most negative) to white (uncharged).

Extended Data Figure 6 Electrostatic surface potential of ABCG2 and comparison of ABCG2 and ABCG5/G8.

a, The molecular surface of ABCG2, colour-coded by electrostatic potential ranging from blue (most positive) to red (most negative) to white (uncharged). The lipid membrane (40 Å) is indicated by the black lines on the basis of the distribution of non-polar residues and transmembrane helices, and the 5D3-Fab binding surface is boxed. b, Overlay of the ABCG2 and ABCG5/G8 TMDs with EL3 boxed. Panels a and b are coloured as in Fig. 2a and ABCG5/G8 is coloured green. c, EL3 sequence alignment of the G-family of ABC transporters with the cysteines involved in disulfide bond formation indicated by red asterisks and with EL3 boxed.

Extended Data Figure 7 Purification of human ABCG2 and pull-down assays of human and rat ABCG2 using the 5D3 monoclonal antibody.

a, Representative SDS–PAGE of purified ABCG2. The same sample was applied after (lane 1) or before (lane 2) disulfide reduction using DTT, demonstrating disulfide-dependent dimerization of ABCG2 (black arrows). M indicates marker proteins, with selected masses indicated on the left. b, Pull-down assay showing that the sepharose-immobilized 5D3-monoclonal antibody does not bind to rat YFP–ABCG2. Human YFP–ABCG2 cell lysate (lane 1), flow-through (lane 2), and elution (lane 3). Rat YFP–ABCG2 cell lysate (lane 4), flow-through (lane 5), and elution (lane 6).

Extended Data Table 1 Summary of cryo-EM data
Extended Data Table 2 Data collection and refinement statistics

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Taylor, N., Manolaridis, I., Jackson, S. et al. Structure of the human multidrug transporter ABCG2. Nature 546, 504–509 (2017). https://doi.org/10.1038/nature22345

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