9CL0 | pdb_00009cl0

Cryo-EM structure of human XPR1 in presence of inorganic phosphate and phytic acid

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  MemProtMDmpstruc

  • Deposited: 2024-07-10 Released: 2025-06-18 
  • Deposition Author(s): Wang, Z., Wu, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

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

Wu, H.Sun, L.Huo, T.Wensel, T.G.Horrigan, F.T.Wang, Z.

(2025) Nat Commun 16: 4519-4519

  • DOI: https://doi.org/10.1038/s41467-025-59678-2
  • Primary Citation of Related Structures:  
    9CKZ, 9CL0

  • PubMed Abstract: 

    Maintaining a balance of inorganic phosphate (Pi) is vital for cellular functionality. Proper phosphate levels are managed through Pi import and export; and the processes governing Pi export remain the least understood. Xenotropic and Polytropic retrovirus Receptor 1 (XPR1) has been identified as the only known Pi export protein in mammals. 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. 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. Further analyses, including the structure of hXPR1 in presence of Pi, and mutagenesis studies at one of the putative Pi binding sites, lead us to propose a plausible ion permeation pathway. Together, our results provide novel perspectives on the Pi transport mechanism of XPR1.


  • Organizational Affiliation
    • Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 53 member 1
A, B
724Homo sapiensMutation(s): 0 
Gene Names: XPR1SLC53A1SYG1X3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBH6 (Homo sapiens)
Explore Q9UBH6 
Go to UniProtKB:  Q9UBH6
PHAROS:  Q9UBH6
GTEx:  ENSG00000143324 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBH6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM143380
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL162842

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release