8YFD | pdb_00008yfd

Cryo EM structure of human phosphate channel XPR1 at open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8YFD

This is version 1.4 of the entry. See complete history

Literature

Structural basis for inositol pyrophosphate gating of the phosphate channel XPR1.

Lu, Y.Yue, C.X.Zhang, L.Yao, D.Xia, Y.Zhang, Q.Zhang, X.Li, S.Shen, Y.Cao, M.Guo, C.R.Qin, A.Zhao, J.Zhou, L.Yu, Y.Cao, Y.

(2024) Science 386: eadp3252-eadp3252

  • DOI: https://doi.org/10.1126/science.adp3252
  • Primary Citation Related Structures: 
    8YET, 8YEX, 8YF4, 8YFD, 8YFU, 8YFW, 8YFX, 9IWS

  • PubMed Abstract: 

    Precise regulation of intracellular phosphate (Pi) is critical for cellular function, with XPR1 serving as the sole Pi exporter in humans. The mechanism of Pi efflux, activated by inositol pyrophosphates (PP-IPs), has remained unclear. This study presents cryo-electron microscopy structures of XPR1 in multiple conformations, revealing a transmembrane pathway for Pi export and a dual-binding activation pattern by PP-IPs. A canonical binding site is located at the dimeric interface of SPX domains, and a second site, biased toward PP-IPs, is found between the transmembrane and SPX domains. By integrating structural studies with electrophysiological analyses, we characterize XPR1 as an IPs/PP-IPs-activated phosphate channel. The interplay among its TMDs, SPX domains, and IPs/PP-IPs orchestrates the conformational transition between its closed and open states.


  • Organizational Affiliation
    • Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China.

Macromolecule Content 

  • Total Structure Weight: 92.94 kDa 
  • Atom Count: 6,588 
  • Modeled Residue Count: 792 
  • Deposited Residue Count: 792 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Solute carrier family 53 member 1
A, B
396Homo 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: 3.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82072468
National Natural Science Foundation of China (NSFC)China82272519
National Natural Science Foundation of China (NSFC)China32371289
National Natural Science Foundation of China (NSFC)China82072468

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references
  • Version 1.3: 2024-12-18
    Changes: Data collection, Database references
  • Version 1.4: 2025-07-16
    Changes: Data collection