9j51

CryoEM structure of human XPR1 in complex with phosphate in state ACryoEM structure of human XPR1 in complex with phosphate in state A

Structural highlights

9j51 is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

S53A1_HUMAN Bilateral striopallidodentate calcinosis. The disease is caused by variants affecting the gene represented in this entry.

Function

S53A1_HUMAN Inorganic ion transporter that mediates phosphate ion export across plasma membrane. Plays a major role in phosphate homeostasis, preventing intracellular phosphate accumulation and possible calcium phosphate precipitation, ultimately preserving calcium signaling. The molecular mechanism of phosphate transport, whether electrogenic, electroneutral or coupled to other ions, remains to be elucidated (By similarity) (PubMed:23791524, PubMed:25938945, PubMed:31043717). Binds inositol hexakisphosphate (Ins6P) and similar inositol polyphosphates, such as 5-diphospho-inositol pentakisphosphate (5-InsP7), important intracellular signaling molecules involved in regulation of phosphate flux (PubMed:27080106).[UniProtKB:Q9Z0U0]^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

XPR1 is the sole protein known to transport inorganic phosphate (Pi) out of cells, a function conserved across species from yeast to mammals. Human XPR1 variants lead to cerebral calcium-phosphate deposition and primary familial brain calcification (PFBC), a hereditary neurodegenerative disorder. Here, we present the cryo-EM structure of human XPR1 in both its Pi-unbound and various Pi-bound states. XPR1 features 10 transmembrane alpha-helices forming an ion channel-like structure, with multiple Pi recognition sites along the channel. Pathogenic mutations in two arginine residues, which line the translocation channel, disrupt Pi transport. Molecular dynamics simulations reveal that Pi ion undergoes a stepwise transition through the sequential recognition sites during the transport process. Together with functional analyses, our results suggest that this sequential arrangement allows XPR1 to facilitate Pi ion passage via a "relay" process, and they establish a framework for the interpretation of disease-related mutations and for the development of future therapeutics.

Structural insights into the mechanism of phosphate recognition and transport by XPR1.,Zhang W, Chen Y, Guan Z, Wang Y, Tang M, Du Z, Zhang J, Cheng M, Zuo J, Liu Y, Wang Q, Liu Y, Zhang D, Yin P, Ma L, Liu Z Nat Commun. 2025 Jan 2;16(1):18. doi: 10.1038/s41467-024-55471-9. PMID:39747008^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Giovannini D, Touhami J, Charnet P, Sitbon M, Battini JL. Inorganic phosphate export by the retrovirus receptor XPR1 in metazoans. Cell Rep. 2013 Jun 27;3(6):1866-73. PMID:23791524 doi:10.1016/j.celrep.2013.05.035
↑ Legati A, Giovannini D, Nicolas G, Lopez-Sanchez U, Quintans B, Oliveira JR, Sears RL, Ramos EM, Spiteri E, Sobrido MJ, Carracedo A, Castro-Fernandez C, Cubizolle S, Fogel BL, Goizet C, Jen JC, Kirdlarp S, Lang AE, Miedzybrodzka Z, Mitarnun W, Paucar M, Paulson H, Pariente J, Richard AC, Salins NS, Simpson SA, Striano P, Svenningsson P, Tison F, Unni VK, Vanakker O, Wessels MW, Wetchaphanphesat S, Yang M, Boller F, Campion D, Hannequin D, Sitbon M, Geschwind DH, Battini JL, Coppola G. Mutations in XPR1 cause primary familial brain calcification associated with altered phosphate export. Nat Genet. 2015 Jun;47(6):579-81. doi: 10.1038/ng.3289. Epub 2015 May 4. PMID:25938945 doi:http://dx.doi.org/10.1038/ng.3289
↑ Wild R, Gerasimaite R, Jung JY, Truffault V, Pavlovic I, Schmidt A, Saiardi A, Jessen HJ, Poirier Y, Hothorn M, Mayer A. Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains. Science. 2016 Apr 14. pii: aad9858. PMID:27080106 doi:http://dx.doi.org/10.1126/science.aad9858
↑ López-Sánchez U, Nicolas G, Richard AC, Maltête D, Charif M, Ayrignac X, Goizet C, Touhami J, Labesse G, Battini JL, Sitbon M. Characterization of XPR1/SLC53A1 variants located outside of the SPX domain in patients with primary familial brain calcification. Sci Rep. 2019 May 1;9(1):6776. PMID:31043717 doi:10.1038/s41598-019-43255-x
↑ Zhang W, Chen Y, Guan Z, Wang Y, Tang M, Du Z, Zhang J, Cheng M, Zuo J, Liu Y, Wang Q, Liu Y, Zhang D, Yin P, Ma L, Liu Z. Structural insights into the mechanism of phosphate recognition and transport by XPR1. Nat Commun. 2025 Jan 2;16(1):18. PMID:39747008 doi:10.1038/s41467-024-55471-9

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OCA

[1] Giovannini D, Touhami J, Charnet P, Sitbon M, Battini JL. Inorganic phosphate export by the retrovirus receptor XPR1 in metazoans. Cell Rep. 2013 Jun 27;3(6):1866-73. PMID:23791524 doi:10.1016/j.celrep.2013.05.035

[2] Legati A, Giovannini D, Nicolas G, Lopez-Sanchez U, Quintans B, Oliveira JR, Sears RL, Ramos EM, Spiteri E, Sobrido MJ, Carracedo A, Castro-Fernandez C, Cubizolle S, Fogel BL, Goizet C, Jen JC, Kirdlarp S, Lang AE, Miedzybrodzka Z, Mitarnun W, Paucar M, Paulson H, Pariente J, Richard AC, Salins NS, Simpson SA, Striano P, Svenningsson P, Tison F, Unni VK, Vanakker O, Wessels MW, Wetchaphanphesat S, Yang M, Boller F, Campion D, Hannequin D, Sitbon M, Geschwind DH, Battini JL, Coppola G. Mutations in XPR1 cause primary familial brain calcification associated with altered phosphate export. Nat Genet. 2015 Jun;47(6):579-81. doi: 10.1038/ng.3289. Epub 2015 May 4. PMID:25938945 doi:http://dx.doi.org/10.1038/ng.3289

[3] Wild R, Gerasimaite R, Jung JY, Truffault V, Pavlovic I, Schmidt A, Saiardi A, Jessen HJ, Poirier Y, Hothorn M, Mayer A. Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains. Science. 2016 Apr 14. pii: aad9858. PMID:27080106 doi:http://dx.doi.org/10.1126/science.aad9858

[4] López-Sánchez U, Nicolas G, Richard AC, Maltête D, Charif M, Ayrignac X, Goizet C, Touhami J, Labesse G, Battini JL, Sitbon M. Characterization of XPR1/SLC53A1 variants located outside of the SPX domain in patients with primary familial brain calcification. Sci Rep. 2019 May 1;9(1):6776. PMID:31043717 doi:10.1038/s41598-019-43255-x

[5] Zhang W, Chen Y, Guan Z, Wang Y, Tang M, Du Z, Zhang J, Cheng M, Zuo J, Liu Y, Wang Q, Liu Y, Zhang D, Yin P, Ma L, Liu Z. Structural insights into the mechanism of phosphate recognition and transport by XPR1. Nat Commun. 2025 Jan 2;16(1):18. PMID:39747008 doi:10.1038/s41467-024-55471-9

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