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- EMDB-61872: Cryo-EM structure of XPR1-KIDINS220 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61872
TitleCryo-EM structure of XPR1-KIDINS220 complex
Map data
Sample
  • Complex: Cryo-EM structure of XPR1-KIDINS220 complex
Keywordsphosphate channel / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 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_61872.png

Downloads & links

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Map

FileDownload / File: emd_61872.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 443.1 Å		1.06 Å/pix.
x 420 pix.
= 443.1 Å		1.06 Å/pix.
x 420 pix.
= 443.1 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: 0.26
Minimum - Maximum-1.9965934 - 2.727791
Average (Standard dev.)0.0007131 (±0.02996545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 443.09998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61872_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #2

Fileemd_61872_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Cryo-EM structure of XPR1-KIDINS220 complex

EntireName: Cryo-EM structure of XPR1-KIDINS220 complex
Components
  • Complex: Cryo-EM structure of XPR1-KIDINS220 complex

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Supramolecule #1: Cryo-EM structure of XPR1-KIDINS220 complex

SupramoleculeName: Cryo-EM structure of XPR1-KIDINS220 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 295825
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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