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- EMDB-61867: Cryo-EM structure of human XPR1 in an open state at the intracell... -

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Basic information

Entry
Database: EMDB / ID: EMD-61867
TitleCryo-EM structure of human XPR1 in an open state at the intracellular gate and a closed state at the extracellular gate, obtained through local refinement
Map data
Sample
  • Complex: Homodimer of XPR1
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: PHOSPHATE ION
Keywordsphosphate channel / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 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, 1 items
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, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61867.png

Downloads & links

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Map

FileDownload / File: emd_61867.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 260 pix.
= 274.3 Å		1.06 Å/pix.
x 260 pix.
= 274.3 Å		1.06 Å/pix.
x 260 pix.
= 274.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.432
Minimum - Maximum-2.005763 - 3.0336404
Average (Standard dev.)0.0052119163 (±0.0635952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 274.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61867_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #2

Fileemd_61867_half_map_2.map
Projections & Slices
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Sample components

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Entire : Homodimer of XPR1

EntireName: Homodimer of XPR1
Components
  • Complex: Homodimer of XPR1
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Homodimer of XPR1

SupramoleculeName: Homodimer of XPR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 53 member 1

MacromoleculeName: Solute carrier family 53 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.164688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKFAEHLSAH ITPEWRKQYI QYEAFKDMLY SAQDQAPSVE VTDEDTVKRY FAKFEEKFFQ TCEKELAKIN TFYSEKLAEA QRRFATLQN ELQSSLDAQK ESTGVTTLRQ RRKPVFHLSH EERVQHRNIK DLKLAFSEFY LSLILLQNYQ NLNFTGFRKI L KKHDKILE ...String:
MKFAEHLSAH ITPEWRKQYI QYEAFKDMLY SAQDQAPSVE VTDEDTVKRY FAKFEEKFFQ TCEKELAKIN TFYSEKLAEA QRRFATLQN ELQSSLDAQK ESTGVTTLRQ RRKPVFHLSH EERVQHRNIK DLKLAFSEFY LSLILLQNYQ NLNFTGFRKI L KKHDKILE TSRGADWRVA HVEVAPFYTC KKINQLISET EAVVTNELED GDRQKAMKRL RVPPLGAAQP APAWTTFRVG LF CGIFIVL NITLVLAAVF KLETDRSIWP LIRIYRGGFL LIEFLFLLGI NTYGWRQAGV NHVLIFELNP RSNLSHQHLF EIA GFLGIL WCLSLLACFF APISVIPTYV YPLALYGFMV FFLINPTKTF YYKSRFWLLK LLFRVFTAPF HKVGFADFWL ADQL NSLSV ILMDLEYMIC FYSLELKWDE SKGLLPNNSE ESGICHKYTY GVRAIVQCIP AWLRFIQCLR RYRDTKRAFP HLVNA GKYS TTFFMVTFAA LYSTHKERGH SDTMVFFYLW IVFYIISSCY TLIWDLKMDW GLFDKNAGEN TFLREEIVYP QKAYYY CAI IEDVILRFAW TIQISITSTT LLPHSGDIIA TVFAPLEVFR RFVWNFFRLE NEHLNNCGEF RAVRDISVA

UniProtKB: Solute carrier family 53 member 1

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Macromolecule #2: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 49.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 946324
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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