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Cryo-EM structures of a human ABCG2 mutant trapped in ATP-bound and substrate-bound states

Abstract

ABCG2 is a transporter protein of the ATP-binding-cassette (ABC) family that is expressed in the plasma membrane in cells of various tissues and tissue barriers, including the blood–brain, blood–testis and maternal–fetal barriers1,2,3,4. Powered by ATP, it translocates endogenous substrates, affects the pharmacokinetics of many drugs and protects against a wide array of xenobiotics, including anti-cancer drugs5,6,7,8,9,10,11,12. Previous studies have revealed the architecture of ABCG2 and the structural basis of its inhibition by small molecules and antibodies13,14. However, the mechanisms of substrate recognition and ATP-driven transport are unknown. Here we present high-resolution cryo-electron microscopy (cryo-EM) structures of human ABCG2 in a substrate-bound pre-translocation state and an ATP-bound post-translocation state. For both structures, we used a mutant containing a glutamine replacing the catalytic glutamate (ABCG2EQ), which resulted in reduced ATPase and transport rates and facilitated conformational trapping for structural studies. In the substrate-bound state, a single molecule of estrone-3-sulfate (E1S) is bound in a central, hydrophobic and cytoplasm-facing cavity about halfway across the membrane. Only one molecule of E1S can bind in the observed binding mode. In the ATP-bound state, the substrate-binding cavity has collapsed while an external cavity has opened to the extracellular side of the membrane. The ATP-induced conformational changes include rigid-body shifts of the transmembrane domains, pivoting of the nucleotide-binding domains (NBDs), and a change in the relative orientation of the NBD subdomains. Mutagenesis and in vitro characterization of transport and ATPase activities demonstrate the roles of specific residues in substrate recognition, including a leucine residue that forms a ‘plug’ between the two cavities. Our results show how ABCG2 harnesses the energy of ATP binding to extrude E1S and other substrates, and suggest that the size and binding affinity of compounds are important for distinguishing substrates from inhibitors.

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Fig. 1: Structures and transport cycle of ABCG2.
Fig. 2: Substrate-binding cavity and mutant analysis.
Fig. 3: ATP-induced conformational changes.
Fig. 4: Substrate-translocation pathway.

Data availability

Atomic coordinates for ABCG2EQ–E1S (including only the variable domain of 5D3-Fab) and ABCG2EQ–ATP were deposited in the Protein Data Bank under accession codes 6HCO and 6HBU, respectively. Electron microscopy data for the two structures were deposited in the Electron Microscopy Data Bank under accession codes EMD-0196 (ABCG2EQ–E1S) and EMD-0190 (ABCG2EQ–ATP). Source Data for Fig. 2e, f and Extended Data Figs. 1e, 2b, d, f and 5 are available online. All other data are available from the corresponding author upon reasonable request. A Life Sciences Reporting Summary for this article is available.

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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 Zurich (ETH Zurich) research grant (ETH-22-14-1). N.M.I.T. was also supported by the Research Fund Junior Researchers of the University of Basel. J.K. was also supported by the TransCure Young Investigator Award (2017). Cryo-EM data were collected at C-CINA, University of Basel; we thank K. Goldie, L. Kováčik and A. Fecteau-Lefebvre for technical support. We thank N. Tremp for help with cell culture and B. Sorrentino (St Jude Children’s Research Hospital) for providing the 5D3-producing hybridoma cell line.

Reviewer information

Nature thanks H. Mchaourab and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Authors and Affiliations

Authors

Contributions

I.M. expressed and purified wild-type ABCG2 and 5D3-Fab. I.M. and S.M.J. cloned, expressed and purified the ABCG2 mutants. S.M.J. reconstituted ABCG2 into liposomes and lipidic nanodiscs for cryo-EM and functional studies and carried out all functional experiments. J.K. prepared cryo-grids. N.M.I.T. collected cryo-EM data with the assistance of H.S. I.M. processed cryo-EM data of ATP-bound ABCG2 and determined the structure with the assistance of J.K. N.M.I.T. processed electron microscopy data and determined the structure of E1S-bound ABCG2. I.M and K.P.L. built, refined and validated the structures. K.P.L., I.M. and S.M.J. conceived the project, designed the experiments and wrote the manuscript. All authors contributed to revision of the manuscript.

Corresponding authors

Correspondence to Henning Stahlberg or Kaspar P. Locher.

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Extended data figures and tables

Extended Data Fig. 1 Purification, activity and cryo-EM micrographs of ABCG2.

a, Preparative SEC profile (milli absorbance units (mAU) at 280 nm plotted against retention volume (ml)) of the nanodisc-reconstituted ABCG2EQ–E1S complex. The fraction used for cryo-EM grid preparation is indicated by a red asterisk. Inset: reducing (lane 1) and non-reducing (lane 2) SDS–PAGE of the complex, showing bands for ABCG2 (G2), 5D3-Fab (Fab) and nanodisc (ND). b, Preparative SEC profile of the nanodisc-reconstituted ABCG2EQ–ATP complex. The fraction used for cryo-EM grid preparation is indicated by a red asterisk. Inset: reducing (lane 1) and non-reducing (lane 2) SDS–PAGE of the complex, showing bands for ABCG2 (G2) and nanodisc (ND). c, An example micrograph (drift-corrected, dose-weighted and low-pass-filtered to 20 Å) of the nanodisc-reconstituted ABCG2EQ–E1S sample. White scale bar, 50 nm. d, An example micrograph (drift-corrected, dose-weighted and low-pass-filtered to 20 Å) of the nanodisc-reconstituted ABCG2EQ–ATP sample. White scale bar, 50 nm. e, ATPase activities of nanodisc-reconstituted and E1S-transport activities of liposome-reconstituted ABCG2. In both cases, data for wild-type and mutant (E211Q) ABCG2 are shown. The standard deviation from n technical replicates (same batch of nanodiscs or liposomes) is shown.

Source data

Extended Data Fig. 2 Effect of 5D3-Fab on ABCG2 function.

a, Analytical SEC profile of the nanodisc-reconstituted ABCG2EQ–E1S complex in the presence of 5 mM ATP and 5 mM MgCl2. ‘1’ denotes the peak collected. Inset: non-reducing SDS–PAGE of the complex, showing bands for ABCG2 (G2), 5D3-Fab (Fab) and nanodisc (ND). b, ATPase activity of liposome-reconstituted ABCG2, in the presence or absence of 5D3-Fab, and with 0–300 µM E1S. The basal ATPase activity has been normalized (norm) to 0. c, As for b, but with the maximal ATPase activity set to 100%. Each point represents the mean rate derived from technical replicates. For G2 n = 6, except in the case of 0 and 200 µM E1S, for which n = 9. For G2 + Fab, n = 3. d, ATPase activities of ABCG2 in the presence and absence of 5D3-Fab, and either 0 or 50 µM E1S. e, As for d, but with activities in the presence of E1S set to 100%. Bars show means and dots show the rates derived from each technical replicate (same batch of liposomes). Error bars show the standard deviation. f, The EC50 of E1S ATPase stimulation determined using the curves in b and c with the error of the fit (standard deviation) shown. PL, proteoliposome.

Source data

Extended Data Fig. 3 Cryo-EM map generation, data processing and atomic-model refinement of ABCG2EQ–E1S.

a, Twelve representative 2D class averages of the final round of 2D classification, sorted in decreasing order by the number of particles assigned to each class. b, FSC from the CryoSPARC auto-refine procedure of the unmasked half-maps (blue), the half-maps after masking (green), and the half-maps after masking and correction for the influence of the mask (pink). A horizontal dotted line (blue) is drawn for the FSC = 0.143 criterion. For both the unmasked and the corrected FSC curves, their intersection with the FSC = 0.143 and the FSC = 0.5 lines are marked by arrows, and the resolutions at these points are indicated. c, FSC curve of the final 3.58 Å refined model versus the map against it was refined (FSCfull; black line). The FSC curve of the final refined model with introduced shifts (mean value of 0.3 Å) versus the first of two independent half-maps (half-map 1, against which it was refined; FSCwork; green line) or the same model versus the second independent half-map (against which it was not refined; FSChalf2; red line) is also shown. d, Flow chart for cryo-EM data processing and structure determination of the ABCG2EQ–E1S complex. e, Full view of the final CryoSPARC B-factor-sharpened map of ABCG2EQ–E1S, coloured by local resolution in Å, as calculated by ResMap with the clipping plane in the middle of the molecule. f, Angular distribution plot for the final reconstruction.

Extended Data Fig. 4 Fit of the models to the densities.

a, Fit of the TM helices of the final model of the ABCG2EQ–E1S TMD to the post-processed and masked C2 map from CryoSPARC. A region of up to 2 Å around the atoms is shown. b, The fit of one E1S molecule (pink or turquoise sticks) in two possible orientations, flipped by 180°, docked into the C2-symmetrized substrate density of the final model of ABCG2EQ–E1S. The contour level has been reduced by comparison with Fig. 2a to show the strongest density at the core of the polycyclic rings. c, As for b, but showing the fit of one E1S into the electron microscopy density of the post-processed and masked C1 map from CryoSPARC. d, Fit of the TM helices of the final model of the ABCG2EQ–ATP TMD to the post-processed and masked C2 map from RELION. A region of up to 2 Å around the atoms is shown.

Extended Data Fig. 5 Purification and functional analysis of mutants.

a, Analytical SEC profiles of the detergent-purified wild-type and substrate-binding cavity mutants used to make proteoliposomes for functional assays. b, ATPase rates of the liposome-reconstituted wild-type and mutant proteins in the presence of 0–300 µM E1S. Each point represents the mean rate derived from technical replicates (same batch of liposomes) and error bars show the standard deviation. For G2, n = 6, except in the case of 0 and 200 µM E1S, for which n = 9. For the mutants, n = 3. c, Table showing the EC50 of E1S ATPase stimulation determined after normalizing the curves in b with the error of the fit (standard deviation) shown.

Source data

Extended Data Fig. 6 Cryo-EM map generation, data processing and atomic-model refinement of ABCG2EQ–ATP.

a, Twelve representative 2D class averages of the final round of 2D classification, sorted in decreasing order by the number of particles assigned to each class. b, FSC from the RELION auto-refine procedure of the unmasked half-maps (blue), the half-maps after masking (green), and the half-maps after masking and correction for the influence of the mask (pink). A horizontal dotted line (blue) is drawn for the FSC = 0.143 criterion. For both the unmasked and the corrected FSC curves, their intersection with the FSC = 0.143 and the FSC = 0.5 lines are marked by arrows, and the resolutions at these points are indicated. c, FSC curve of the final 3.09 Å refined model versus the map against which it was refined (FSCfull; black line). FSC curves of the final refined model with introduced shifts (mean value of 0.3 Å) versus the first of two independent half-maps (half-map 1, against which it was refined; FSCwork; green line) or the same model versus the second independent half-map (against which it was not refined; FSChalf2; red line) are also shown. d, Flow chart for cryo-EM data processing and structure determination of the ABCG2EQ–ATP complex. The map used for model building is indicated by a red square. e, Full view of the RELION local-resolution-filtered map of ABCG2EQ–ATP, coloured by local resolution in Å as calculated by ResMap, with the clipping plane in the middle of the molecule. f, Angular distribution plot for the final reconstruction.

Extended Data Table 1 Cryo-EM data collection, refinement and validation statistics

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Manolaridis, I., Jackson, S.M., Taylor, N.M.I. et al. Cryo-EM structures of a human ABCG2 mutant trapped in ATP-bound and substrate-bound states. Nature 563, 426–430 (2018). https://doi.org/10.1038/s41586-018-0680-3

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Keywords

  • Human ABCG2
  • Substrate-bound State
  • Substrate-binding Cavity
  • Nucleotide-binding Domain (NBD)
  • External Cavity

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