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- PDB-9jxg: Cryo-EM structure of apo human XPR1, class 3, with symmetrically ... -

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Basic information

Entry
Database: PDB / ID: 9jxg
TitleCryo-EM structure of apo human XPR1, class 3, with symmetrically dimerized SPX domains
ComponentsSolute carrier family 53 member 1
KeywordsTRANSPORT PROTEIN / phosphate channel / phosphate exporter / PFBC
Function / homology
Function and homology information


phosphate transmembrane transporter activity / phosphate ion transport / intracellular phosphate ion homeostasis / phosphate ion transmembrane transport / cellular response to phosphate starvation / inositol hexakisphosphate binding / efflux transmembrane transporter activity / response to virus / virus receptor activity / plasma membrane
Similarity search - Function
EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
Solute carrier family 53 member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsWang, X. / Bai, Z. / Wallis, C. / Wang, H. / Han, Y. / Jin, R. / Lei, M. / Gu, C. / Jessen, H. / Shears, 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 support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022ZD0207400 China
CitationJournal: Mol Cell / Year: 2025
Title: KIDINS220 and InsP8 safeguard the stepwise regulation of phosphate exporter XPR1.
Authors: Xiaojie Wang / Zhongjian Bai / Ciara Wallis / Huanchen Wang / Yaoyao Han / Ruitao Jin / Mingguang Lei / Tian Yang / Chunfang Gu / Henning Jessen / Stephen Shears / Yadong Sun / Ben Corry / Yixiao Zhang /
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 ...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.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Sep 17, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Solute carrier family 53 member 1
B: Solute carrier family 53 member 1


Theoretical massNumber of molelcules
Total (without water)163,2702
Polymers163,2702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Solute carrier family 53 member 1 / Phosphate exporter SLC53A1 / Protein SYG1 homolog / Xenotropic and polytropic murine leukemia virus ...Phosphate exporter SLC53A1 / Protein SYG1 homolog / Xenotropic and polytropic murine leukemia virus receptor X3 / X-receptor / Xenotropic and polytropic retrovirus receptor 1


Mass: 81634.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPR1, SLC53A1, SYG1, X3 / Production host: Homo sapiens (human) / References: UniProt: Q9UBH6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homodimer of XPR1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49.41 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1Gautomatchparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103528 / Symmetry type: POINT
RefinementHighest resolution: 3.75 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0139952
ELECTRON MICROSCOPYf_angle_d1.03413479
ELECTRON MICROSCOPYf_dihedral_angle_d5.261272
ELECTRON MICROSCOPYf_chiral_restr0.0371463
ELECTRON MICROSCOPYf_plane_restr0.0051674

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