8X5B | pdb_00008x5b

Cryo-EM structures of human XPR1 in closed states


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8X5B

This is version 1.4 of the entry. See complete history

Literature

Human XPR1 structures reveal phosphate export mechanism.

Yan, R.Chen, H.Liu, C.Zhao, J.Wu, D.Jiang, J.Gong, J.Jiang, D.

(2024) Nature 633: 960-967

  • DOI: https://doi.org/10.1038/s41586-024-07852-9
  • Primary Citation Related Structures: 
    8X5B, 8X5E, 8X5F

  • PubMed Abstract: 

    Inorganic phosphate (Pi) is a fundamental macronutrient for all living organisms, the homeostasis of which is critical for numerous biological activities 1-3 . As the only known human Pi exporter to date, XPR1 has an indispensable role in cellular Pi homeostasis 4,5 . Dysfunction of XPR1 is associated with neurodegenerative disease 6-8 . However, the mechanisms underpinning XPR1-mediated Pi efflux and regulation by the intracellular inositol polyphosphate (InsPP) sensor SPX domain remain poorly understood. Here we present cryo-electron microscopy structures of human XPR1 in Pi-bound closed, open and InsP 6 -bound forms, revealing the structural basis for XPR1 gating and regulation by InsPPs. XPR1 consists of an N-terminal SPX domain, a dimer-formation core domain and a Pi transport domain. Within the transport domain, three basic clusters are responsible for Pi binding and transport, and a conserved W573 acts as a molecular switch for gating. In addition, the SPX domain binds to InsP 6 and facilitates Pi efflux by liberating the C-terminal loop that limits Pi entry. This study provides a conceptual framework for the mechanistic understanding of Pi homeostasis by XPR1 homologues in fungi, plants and animals.


  • Organizational Affiliation
    • Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 124.88 kDa 
  • Atom Count: 6,973 
  • Modeled Residue Count: 786 
  • Deposited Residue Count: 936 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Solute carrier family 53 member 1A [auth F],
B [auth A]
468Homo sapiensMutation(s): 0 
Gene Names: XPR1
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
(Subject of Investigation/LOI)

Query on POV



Download:Ideal Coordinates CCD File
AA [auth A]
CA [auth A]
DA [auth A]
G [auth F]
H [auth F]
AA [auth A],
CA [auth A],
DA [auth A],
G [auth F],
H [auth F],
I [auth F],
J [auth F],
K [auth F],
M [auth F],
N [auth F],
O [auth F],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
BA [auth A],
L [auth F]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth F]
D [auth F]
E [auth F]
F
P [auth A]
C [auth F],
D [auth F],
E [auth F],
F,
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 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)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Data collection, Database references
  • Version 1.2: 2024-09-04
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.4: 2025-07-02
    Changes: Data collection