9IUC | pdb_00009iuc

Cryo-EM structure of human XPR1 in complex with InsP6 in closed state - in the presence of KIDINS220-1-432 without substrate KH2PO4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Synergistic activation of the human phosphate exporter XPR1 by KIDINS220 and inositol pyrophosphate.

Zuo, P.Wang, W.Dai, Z.Zheng, J.Yu, S.Wang, G.Yin, Y.Liang, L.Yin, Y.

(2025) Nat Commun 16: 2879-2879

  • DOI: https://doi.org/10.1038/s41467-025-58200-y
  • Primary Citation of Related Structures:  
    9INE, 9INF, 9INH, 9ITG, 9IUC

  • PubMed Abstract: 

    Inorganic phosphate (Pi) is essential for life, and its intracellular levels must be tightly regulated to avoid toxicity. XPR1, the sole known phosphate exporter, is critical for maintaining this balance. Here we report cryo-EM structures of the human XPR1-KIDINS220 complex in substrate-free closed and substrate-bound outward-open states, as well as an XPR1 mutant in a substrate-bound inward-facing state. In the presence of inositol hexaphosphate (InsP 6 ) and phosphate, the complex adopts an outward-open conformation, with InsP 6 binding the SPX domain and juxtamembrane regions, indicating active phosphate export. Without phosphate or InsP 6 , the complex closes, with transmembrane helix 9 blocking the outward cavity and a C-terminal loop obstructing the intracellular cavity. XPR1 alone remains closed even with phosphate and InsP 6 . Functional mutagenesis shows that InsP 6 , whose levels vary with Pi availability, works with KIDINS220 to regulate XPR1 activity. These insights into phosphate regulation may aid in developing therapies for ovarian cancer.


  • Organizational Affiliation

    Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 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
704Homo 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
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PE (Subject of Investigation/LOI)
Query on 3PE

Download Ideal Coordinates CCD File 
E [auth A]
J [auth A]
O [auth A]
Q [auth B]
T [auth B]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
D [auth A],
S [auth B]
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
ACD (Subject of Investigation/LOI)
Query on ACD

Download Ideal Coordinates CCD File 
AA [auth B],
M [auth A]
ARACHIDONIC ACID
C20 H32 O2
YZXBAPSDXZZRGB-DOFZRALJSA-N
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
BA [auth B],
K [auth A],
N [auth A],
Y [auth B]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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: 2025-04-02
    Type: Initial release