8TYV

Crystal structure of the SPX domain of XPR1 in complex with IP8

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-08-25 Released: 2024-06-12 
  • Deposition Author(s): Wang, H., Shears, S.B.
  • Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Homeostatic coordination of cellular phosphate uptake and efflux requires an organelle-based receptor for the inositol pyrophosphate IP8.

Li, X.Kirkpatrick, R.B.Wang, X.Tucker, C.J.Shukla, A.Jessen, H.J.Wang, H.Shears, S.B.Gu, C.

(2024) Cell Rep 43: 114316-114316

  • DOI: https://doi.org/10.1016/j.celrep.2024.114316
  • Primary Citation of Related Structures:  
    8TYU, 8TYV

  • PubMed Abstract: 

    Phosphate (Pi) serves countless metabolic pathways and is involved in macromolecule synthesis, energy storage, cellular signaling, and bone maintenance. Herein, we describe the coordination of Pi uptake and efflux pathways to maintain mammalian cell Pi homeostasis. We discover that XPR1, the presumed Pi efflux transporter, separately supervises rates of Pi uptake. This direct, regulatory interplay arises from XPR1 being a binding partner for the Pi uptake transporter PiT1, involving a predicted transmembrane helix/extramembrane loop in XPR1, and its hitherto unknown localization in a subset of intracellular LAMP1-positive puncta (named "XLPVs"). A pharmacological mimic of Pi homeostatic challenge is sensed by the inositol pyrophosphate IP 8 , which functionalizes XPR1 to respond in a temporally hierarchal manner, initially adjusting the rate of Pi efflux, followed subsequently by independent modulation of PiT1 turnover to reset the rate of Pi uptake. These observations generate a unifying model of mammalian cellular Pi homeostasis, expanding opportunities for therapeutic intervention.


  • Organizational Affiliation

    Inositol Signaling Group, Signal Transduction Laboratory, National Institute of Environmental, Health Sciences, Research Triangle Park, NC 27709, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 53 member 1A [auth B],
B [auth A]
181Homo sapiensMutation(s): 0 
Gene Names: XPR1SLC53A1SYG1X3
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I8P (Subject of Investigation/LOI)
Query on I8P

Download Ideal Coordinates CCD File 
C [auth A](1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)]
C6 H20 O30 P8
HHQOOERQSFJGEP-SLWYWOEDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.712α = 90
b = 47.754β = 104.21
c = 70.373γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIAES080046

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-12
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Database references, Structure summary