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TitleTransport and InsP gating mechanisms of the human inorganic phosphate exporter XPR1.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 2770, Year 2025
Publish dateMar 20, 2025
AuthorsQinyu Zhu / Madeleine F Yaggi / Nikolaus Jork / Henning J Jessen / Melinda M Diver /
PubMed AbstractInorganic phosphate (Pi) has essential metabolic and structural roles in living organisms. The Pi exporter, XPR1/SLC53A1, is critical for cellular Pi homeostasis. When intercellular Pi is high, cells ...Inorganic phosphate (Pi) has essential metabolic and structural roles in living organisms. The Pi exporter, XPR1/SLC53A1, is critical for cellular Pi homeostasis. When intercellular Pi is high, cells accumulate inositol pyrophosphate (1,5-InsP), a signaling molecule required for XPR1 function. Inactivating XPR1 mutations lead to brain calcifications, causing neurological symptoms including movement disorders, psychosis, and dementia. Here, cryo-electron microscopy structures of dimeric XPR1 and functional characterization delineate the substrate translocation pathway and how InsP initiates Pi transport. Binding of InsP to XPR1, but not the related inositol polyphosphate InsP, rigidifies the intracellular SPX domains, with InsP bridging the dimers and SPX and transmembrane domains. Locked in this state, the C-terminal tail is sequestered, revealing the entrance to the transport pathway, thus explaining the obligate roles of the SPX domain and InsP. Together, these findings advance our understanding of XPR1 transport activity and expand opportunities for rationalizing disease mechanisms and therapeutic intervention.
External linksNat Commun / PubMed:40113814 / PubMed Central
MethodsEM (single particle)
Resolution2.52 - 3.3 Å
Structure data

EMDB-47207: Structure of the phosphate exporter XPR1/SLC53A1, high Pi and InsP6-bound
Method: EM (single particle) / Resolution: 3.3 Å

47208

9dvj

EMDB-47208: Structure of the phosphate exporter XPR1/SLC53A1, apo state
PDB-9dvj: "Structure of the phosphate exporter XPR1/SLC53A1
Method: EM (single particle) / Resolution: 2.52 Å

47209

9dvk

EMDB-47209: Structure of the phosphate exporter XPR1/SLC53A1, apo state, rotated dimer
PDB-9dvk: Structure of the phosphate exporter XPR1/SLC53A1, rotated dimer
Method: EM (single particle) / Resolution: 3.06 Å

47210

9dvl

EMDB-47210, PDB-9dvl:
Structure of the phosphate exporter XPR1/SLC53A1, InsP6-supplemented
Method: EM (single particle) / Resolution: 2.97 Å

47211

9dvm

EMDB-47211: Structure of the phosphate exporter XPR1/SLC53A1, InsP8-bound, inward-open/occluded state
PDB-9dvm: Structure of the phosphate exporter XPR1/SLC53A1, InsP8-bound, intracellular gate open/intracellular gate closed state
Method: EM (single particle) / Resolution: 2.92 Å

47212

9dvn

EMDB-47212: Structure of the phosphate exporter XPR1/SLC53A1, InsP8-bound, occluded state
PDB-9dvn: Structure of the phosphate exporter XPR1/SLC53A1, InsP8-bound, intracellular gate closed state
Method: EM (single particle) / Resolution: 2.75 Å

47213

9dvo

EMDB-47213: Structure of the phosphate exporter XPR1/SLC53A1, Pi and InsP8-bound, inward-open/occluded state
PDB-9dvo: Structure of the phosphate exporter XPR1/SLC53A1, Pi and InsP8-bound, intracellular gate open/intracellular gate closed state
Method: EM (single particle) / Resolution: 3.1 Å

47214

9dvp

EMDB-47214: Structure of the phosphate exporter XPR1/SLC53A1, Pi and InsP8-bound, occluded state
PDB-9dvp: Structure of the phosphate exporter XPR1/SLC53A1, Pi and InsP8-bound, intracellular gate closed state
Method: EM (single particle) / Resolution: 2.81 Å

Chemicals

ChemComp-PO4:
PHOSPHATE ION

ChemComp-CLR:
CHOLESTEROL

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

ChemComp-I8P:
(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)]

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
KeywordsTRANSPORT PROTEIN / Inorganic phosphate exporter

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