9J52 | pdb_00009j52

CryoEM structure of human XPR1 in complex with phosphate in state B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

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.

(2025) Nat Commun 16: 18-18

  • DOI: https://doi.org/10.1038/s41467-024-55471-9
  • Primary Citation of Related Structures:  
    9J4X, 9J51, 9J52, 9J53

  • PubMed Abstract: 

    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 α-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.


  • Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 53 member 1
A, B
720Homo 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: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release