9IJY

Homo sapiens Xenotropic and Polytropic Retrovirus Receptor 1 (XPR1) with Y22A/E23A/K26A mutations

Summary for 9IJY

• Entry DOI: 10.2210/pdb9ijy/pdb
• EMDB information: 60645
• Descriptor: Solute carrier family 53 member 1, PHOSPHATE ION, (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE (3 entities in total)
• Functional Keywords: pi exporter, a key regulator of cellular pi homeostasis, protein transport
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 167943.03

Authors

He, Q.X.,Zhang, R.,Chen, Q.F.,Li, B.B. (deposition date: 2024-06-25, release date: 2025-01-22)

Primary citation

He, Q.,Zhang, R.,Tury, S.,Courgnaud, V.,Liu, F.,Battini, J.L.,Li, B.,Chen, Q.
Structural basis of phosphate export by human XPR1.
Nat Commun, 16:683-683, 2025

PubMed Abstract: Phosphorus in crucial for all living organisms. In vertebrate, cellular phosphate homeostasis is partly controlled by XPR1, a poorly characterized inositol pyrophosphate-dependent phosphate exporter. Here, we report the cryo-EM structure of human XPR1, which forms a loose dimer with 10 transmembrane helices (TM) in each protomer. The structure consists of a scaffold domain (TM1, TM3-4) and a core domain (TM2, TM5-10) structurally related to ion-translocating rhodopsins. Bound phosphate is observed in a tunnel within the core domain at a narrow point that separates the tunnel into intracellular and extracellular vestibules. This site contains a cluster of basic residues that coordinate phosphate and a conserved W573 essential for export function. Loss of inositol pyrophosphate binding is accompanied by structural movements in TM9 and the W573 sidechain, closing the extracellular vestibule and blocking phosphate export. These findings provide insight into XPR1 mechanism and pave the way for further in-depth XPR1 studies.

PubMed: 39814721
DOI: 10.1038/s41467-025-55995-8

Experimental method

ELECTRON MICROSCOPY (2.64 Å)