9JXM | pdb_00009jxm

Cryo-EM structure of one subunit of the human XPR1 homodimer with both the intracellular and extracellular gates in an open state, obtained through local refinement

• PDB DOI: https://doi.org/10.2210/pdb9JXM/pdb
• EM Map EMD-61868: EMDB EMDataResource

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


• Deposited: 2024-10-11 Released: 2025-08-27 
• Deposition Author(s): Wang, X., Bai, Z., Wallis, C., Wang, H., Han, Y., Jin, R., Lei, M., Gu, C., Jessen, H., Shears, S., Sun, Y., Corry, B., Zhang, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

KIDINS220 and InsP8 safeguard the stepwise regulation of phosphate exporter XPR1.

Wang, X., Bai, Z., Wallis, C., Wang, H., Han, Y., Jin, R., Lei, M., Yang, T., Gu, C., Jessen, H., Shears, S., Sun, Y., Corry, B., Zhang, Y.

(2025) Mol Cell 85: 3209-3224.e8

• PubMed: 40858110 
• DOI: https://doi.org/10.1016/j.molcel.2025.08.003
• Primary Citation of Related Structures:  
  9JXD, 9JXE, 9JXF, 9JXG, 9JXH, 9JXI, 9JXJ, 9JXK, 9JXL, 9JXM, 9JXN, 9JXO, 9JXP, 9JXQ, 9JXR


• PubMed Abstract: 
  

  XPR1 is emerging as the only known inorganic phosphate (Pi) exporter in humans, critical for Pi homeostasis, with its activity stimulated by inositol pyrophosphate InsP8 and regulated by neuronal scaffold protein KIDINS220. Our structural studies reveal that InsP8 specifically activates XPR1 in a stepwise manner, involving profound SYG1/PHO/XPR1 (SPX) domain movements. Each XPR1 subunit functions with four gating states, in which Pi permeates a constriction site via a "knock-kiss-kick" process. By contrast, KIDINS220 delicately stabilizes XPR1 in a closed conformation through multiple mechanisms, one of which involves trapping the XPR1 α1 helix-critical for InsP8 binding-within an interaction hub. InsP8 serves as a key to release KIDINS220's restraint, reinforcing a "key-to-locks" mechanism to safeguard the stepwise activation. Additionally, our study provides direct structural insights into XPR1-associated neuronal disorders and highlights the evolutionary conservation and divergence among XPR1 orthologs, offering a comprehensive understanding of Pi homeostasis across species.

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Organizational Affiliation: 
• Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China.
Research School of Biology, Australian National University, Arts and Culture Trust, Acton 2601, Australia.
Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
Eastern Hepatobiliary Surgery Hospital, No. 225, Changhai Road, Shanghai 200438, China.
Institute of Organic Chemistry, University of Freiburg, Albertstraße 21, 79104, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA. Electronic address: [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. Electronic address: [e-mail].
Research School of Biology, Australian National University, Arts and Culture Trust, Acton 2601, Australia. Electronic address: [e-mail].
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Key Laboratory of Aging Studies, Shanghai 201210, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 74.35 kDa 
• Atom Count: 5,063 
• Modeled Residue Count: 609 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 53 member 1	A [auth B]	632	Homo sapiens	Mutation(s): 0  Gene Names: XPR1, SLC53A1, SYG1, X3 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	B, C [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.48 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Wang, X., Bai, Z., Wallis, C., Wang, H., Han, Y., Jin, R., Lei, M., Gu, C., Jessen, H., Shears, S., Sun, Y., Corry, B., Zhang, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022ZD0207400

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release
  
• Version 1.1: 2025-09-10
  Changes: Data collection, Database references
• Version 1.2: 2025-09-17
  Changes: Data collection, Database references