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Cited by 8Ion channel regulation and functionIon Transport and Channel RegulationErythrocyte Function and Pathophysiology

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The identification of XPR1 as a voltage- and phosphate-activated phosphate-permeable ion channel

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Wu, Hongjiang, Sun, Liang, Huo, Tong, Wensel, Theodore G., Horrigan, Frank T., Wang, Zhao·2025·Nature Communications
DOI 10.1038/s41467-025-59678-2PMC PMC12081713

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Abstract

Maintaining a balance of inorganic phosphate (Pi) is vital for cellular functionality due to Pi's essential role in numerous biological processes. Proper phosphate levels are managed through Pi import and export, facilitated by specific Pi transport proteins. Although the mechanisms of Pi import have been extensively studied, the processes governing Pi export remain less understood. Xenotropic and Polytropic retrovirus Receptor 1 (XPR1) has been identified as the only known Pi export protein in mammals, playing a key role in facilitating Pi efflux from cells. Malfunctions in XPR1 are associated with human diseases, such as primary familial brain calcification and certain cancers, highlighting its critical role in maintaining Pi homeostasis. In this study, we introduce the cryogenic electron microscopy structure of human XPR1 (hXPR1), unveiling a structural arrangement distinct from that of any known ion transporter, with a topology not identified in previous computational predictions. Our structural results suggest that hXPR1 may operate as an ion channel, a hypothesis supported by patch clamp recordings revealing hXPR1's voltage- and Pi-dependent activity and large unitary conductance. Using proteoliposomal uptake assays, we demonstrate that purified and reconstituted hXPR1 catalyzes transport of Pi. Further analysis, including the structure of hXPR1 in presence of Pi, and functional effects of mutating a putative Pi binding site, leads us to propose a plausible ion permeation pathway. Together, our results provide novel perspectives on the Pi transport mechanism of XPR1 and its homologues.

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Fig. 1 Overall structure of apo-hXPR1. a The composite Cryo-EM density map (left) and cartoon representations of the atomic model (middle and right) of apo-hXPR1 dimer viewed in the membrane plane from two orthogonal directions. Two protomers are colored magenta and lavender. The densities of the cytosolic domain and TMD are displayed at a contour level of 8.17σ and 5.04σ, respectively. The gray box in the background indicates the membrane bilayer. b Cartoon representations of an hXPR1 monomer viewed from the side and from top-down. The SPX domain is colored in yellow, the EXS domain in light blue, and the rest of the protein in gray. c Topology of a monomeric hXPR1.
Fig. 1 Overall structure of apo-hXPR1. a The composite Cryo-EM density map (left) and cartoon representations of the atomic model (middle and right) of apo-hXPR1 dimer viewed in the membrane plane from two orthogonal directions. Two protomers are colored magenta and lavender. The densities of the cytosolic domain and TMD are displayed at a contour level of 8.17σ and 5.04σ, respectively. The gray box in the background indicates the membrane bilayer. b Cartoon representations of an hXPR1 monomer viewed from the side and from top-down. The SPX domain is colored in yellow, the EXS domain in light blue, and the rest of the protein in gray. c Topology of a monomeric hXPR1.CC BY-NC-ND · PubMed Central
Fig. 2 XPR1 exhibits voltage- and Pi-dependent ion channel activity and Pi transport. a Inwardly-rectifying currents evoked from an excised GUV patch with hXPR1 by voltage ramps (−105 mV to +75 mV) from +15 mV. b Inward currents are evoked by hyperpolarizing voltage-pulses (−15 to −105 mV, in 10 mV intervals) from +95 mV in a GUV patch with hXPR1, but not in detergent control. c Outward tail current at +15 mV following 1 s hyperpolarizing pulses. d Normalized hXPR1 G-V relation from tail currents (mean ± SEM, n = 3 replicates from one GUV) fit by a Boltzmann function (z = −1.8 ± 0.2 e, V1/2 = −34 ± 2 mV, mean ± SD). e Unitary current activity during voltage ramps or +40 mV pulses from a HEK293S GnTI- cell expressing hXPR1. a–e were from inside-out patches with external 0 Pi NMDG-MSA and internal 20 Pi, 0.07 Ca2+, K-MSA solutions. f Unitary XPR1 current recorded from HEK293 cell with single open level and associated all-points histogram at −50 mV with external 1 Pi NMDG-citrate and internal 20 Pi, 0.07 Ca2+, K-MSA solutions. g XPR1 currents evoked from a GUV patch by voltage ramps with 75 mM Pi as the sole internal anion (black) or with 75 mM Pi + 10 Cl− (red) are superimposable. XPR1 currents evoked from a GUV patch by voltage ramps (h) or –50 mV pulses (i) are enhanced as internal Pi is increased from 10 mM (blue) to 75 mM (red), and almost undetectable in 0 Pi (black) using internal 10 Cl K-MSA with external 0 Pi NMDG-MSA solutions. Thick curves represent an average of 5 (g) or 10 (h, i) traces (thin curves). j G-V relations in 10 and 75 mM Pi (mean±SEM, n = 3 patches). G-Vs at both [Pi] were normalized to the maximal conductance in 75 mM Pi. k Schematics of the [32P] Pi transport assay with proteoliposomes. A membrane voltage potential difference was generated using a potassium gradient and valinomycin. l Time-dependent accumulation (mean±SEM, n = 6 independent assays) of [32P] Pi in hXPR1-containing proteoliposomes without valinomycin (blue), with valinomycin (red), and in empty liposomes with valinomycin (black) as control.
Fig. 2 XPR1 exhibits voltage- and Pi-dependent ion channel activity and Pi transport. a Inwardly-rectifying currents evoked from an excised GUV patch with hXPR1 by voltage ramps (−105 mV to +75 mV) from +15 mV. b Inward currents are evoked by hyperpolarizing voltage-pulses (−15 to −105 mV, in 10 mV intervals) from +95 mV in a GUV patch with hXPR1, but not in detergent control. c Outward tail current at +15 mV following 1 s hyperpolarizing pulses. d Normalized hXPR1 G-V relation from tail currents (mean ± SEM, n = 3 replicates from one GUV) fit by a Boltzmann function (z = −1.8 ± 0.2 e, V1/2 = −34 ± 2 mV, mean ± SD). e Unitary current activity during voltage ramps or +40 mV pulses from a HEK293S GnTI- cell expressing hXPR1. a–e were from inside-out patches with external 0 Pi NMDG-MSA and internal 20 Pi, 0.07 Ca2+, K-MSA solutions. f Unitary XPR1 current recorded from HEK293 cell with single open level and associated all-points histogram at −50 mV with external 1 Pi NMDG-citrate and internal 20 Pi, 0.07 Ca2+, K-MSA solutions. g XPR1 currents evoked from a GUV patch by voltage ramps with 75 mM Pi as the sole internal anion (black) or with 75 mM Pi + 10 Cl− (red) are superimposable. XPR1 currents evoked from a GUV patch by voltage ramps (h) or –50 mV pulses (i) are enhanced as internal Pi is increased from 10 mM (blue) to 75 mM (red), and almost undetectable in 0 Pi (black) using internal 10 Cl K-MSA with external 0 Pi NMDG-MSA solutions. Thick curves represent an average of 5 (g) or 10 (h, i) traces (thin curves). j G-V relations in 10 and 75 mM Pi (mean±SEM, n = 3 patches). G-Vs at both [Pi] were normalized to the maximal conductance in 75 mM Pi. k Schematics of the [32P] Pi transport assay with proteoliposomes. A membrane voltage potential difference was generated using a potassium gradient and valinomycin. l Time-dependent accumulation (mean±SEM, n = 6 independent assays) of [32P] Pi in hXPR1-containing proteoliposomes without valinomycin (blue), with valinomycin (red), and in empty liposomes with valinomycin (black) as control.CC BY-NC-ND · PubMed Central
Fig. 3 The putative pore of hXPR1. a (left) The solvent-accessible surface of the hXPR1 TMD colored by ±5 kT/e electrostatic potential calculated using APBS62. The secondary structures of TM1-4 are shown in gray and TM5-10 in light cyan. The positively charged vestibule formed at the center of the barrel-shaped helical bundle of TM5-10 is boxed in red. Two solid black lines indicate the membrane boundary. (right) The electrostatic surface–potential map depicts the same vestibule alone, viewed orthogonally from the extracellular space. b The putative pore location in hXPR1 inside the 6-helix barrel colored light cyan, and the pore pathway is depicted as a purple mesh. The residues on the TM5-10 that are conserved among hXPR1, atPHO1, and scSYG1 are colored in dark green. c Pore radius along the z coordinate. d, e Detailed view of the green-colored conserved pore-lining residues shown in stick model on TM5, 7, and 9 (d), and TM6, 8, and 10 (e).
Fig. 3 The putative pore of hXPR1. a (left) The solvent-accessible surface of the hXPR1 TMD colored by ±5 kT/e electrostatic potential calculated using APBS62. The secondary structures of TM1-4 are shown in gray and TM5-10 in light cyan. The positively charged vestibule formed at the center of the barrel-shaped helical bundle of TM5-10 is boxed in red. Two solid black lines indicate the membrane boundary. (right) The electrostatic surface–potential map depicts the same vestibule alone, viewed orthogonally from the extracellular space. b The putative pore location in hXPR1 inside the 6-helix barrel colored light cyan, and the pore pathway is depicted as a purple mesh. The residues on the TM5-10 that are conserved among hXPR1, atPHO1, and scSYG1 are colored in dark green. c Pore radius along the z coordinate. d, e Detailed view of the green-colored conserved pore-lining residues shown in stick model on TM5, 7, and 9 (d), and TM6, 8, and 10 (e).CC BY-NC-ND · PubMed Central
Fig. 4 Putative ion coordination sites. a The density map of TM5-10 of Pi/InsP6-hXPR1, with each TM helix colored individually at a contour level of 10.96σ. The non-protein isolated densities within the pore are colored in pink red. Densities from TM5 and TM10 (right), or TM7 and TM8 (left), are removed to expose the pore. b The string of putative ion densities in gray depicted at a 10.96σ contour level with the cartoon representation of Pi/InsP6-hXPR1 TM5-10 structure. Densities corresponding to the two putative ion coordination sites are boxed in red and blue. c, d Close-up views of the two putative ion coordination sites indicated in the colored boxes in (b), with the ion density shown at a 5.35σ contour level. e Relative Pi transport of the alanine mutations of three arginine residues within the red-colored putative Pi binding in (c). The relative transport was measured at the 20-min time point with the addition of valinomycin. Means ± SEM plotted (n = 4 independent assays). f XPR1 R570A currents evoked from a GUV patch by voltage ramps are decreased as internal Pi is increased from 10 mM (black) to 75 mM (red), using 10 Cl K-MSA internal solutions with external 0 Pi, 10 NMDG-Cl. Each curve represents the average of 5 traces (as in Fig. 2g).
Fig. 4 Putative ion coordination sites. a The density map of TM5-10 of Pi/InsP6-hXPR1, with each TM helix colored individually at a contour level of 10.96σ. The non-protein isolated densities within the pore are colored in pink red. Densities from TM5 and TM10 (right), or TM7 and TM8 (left), are removed to expose the pore. b The string of putative ion densities in gray depicted at a 10.96σ contour level with the cartoon representation of Pi/InsP6-hXPR1 TM5-10 structure. Densities corresponding to the two putative ion coordination sites are boxed in red and blue. c, d Close-up views of the two putative ion coordination sites indicated in the colored boxes in (b), with the ion density shown at a 5.35σ contour level. e Relative Pi transport of the alanine mutations of three arginine residues within the red-colored putative Pi binding in (c). The relative transport was measured at the 20-min time point with the addition of valinomycin. Means ± SEM plotted (n = 4 independent assays). f XPR1 R570A currents evoked from a GUV patch by voltage ramps are decreased as internal Pi is increased from 10 mM (black) to 75 mM (red), using 10 Cl K-MSA internal solutions with external 0 Pi, 10 NMDG-Cl. Each curve represents the average of 5 traces (as in Fig. 2g).CC BY-NC-ND · PubMed Central

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Metadata

Authors
Wu, H., Sun, L., Huo, T., Wensel, T. G., Horrigan, F. T., & Wang, Z.
Affiliations
  • Baylor College of Medicine (US)
  • The University of Texas MD Anderson Cancer Center (US)
Corresponding author
  • Horrigan, Frank T.
  • Wang, Zhao
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2025-05-15
Volume
16
Issue
1
Pages
4519-4519
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-025-59678-2
PMC
PMC12081713
OpenAlex
W4410401585
Cited by
8
References
62
Citations by year
2026: 4 · 2025: 2
FWCI
1.80
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
  • Digital Commons-TMC (Texas Medical Center) (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (R01HL162842)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ion channel regulation and function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ion Transport and Channel Regulation
  • Health Sciences › Medicine › Physiology (medical) › Erythrocyte Function and Pathophysiology
Keywords
XPR1, phosphate export, inorganic phosphate transport, ion channels, cryo-EM structure, voltage-gated ion channels, phosphate binding site, ion permeation pathway, single-channel conductance, membrane protein structure

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