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- EMDB-61875: Complex of XPR1-KIDINS220 -

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Basic information

Entry
Database: EMDB / ID: EMD-61875
TitleComplex of XPR1-KIDINS220
Map data
Sample
  • Complex: Complex of XPR1-KIDINS220
    • Protein or peptide: Kinase D-interacting substrate of 220 kDa
    • Protein or peptide: Solute carrier family 53 member 1
Keywordsphosphate channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


phosphate transmembrane transporter activity / nerve growth factor signaling pathway / phosphate ion transport / intracellular phosphate ion homeostasis / ARMS-mediated activation / phosphate ion transmembrane transport / cellular response to phosphate starvation / protein kinase regulator activity / inositol hexakisphosphate binding / RND1 GTPase cycle ...phosphate transmembrane transporter activity / nerve growth factor signaling pathway / phosphate ion transport / intracellular phosphate ion homeostasis / ARMS-mediated activation / phosphate ion transmembrane transport / cellular response to phosphate starvation / protein kinase regulator activity / inositol hexakisphosphate binding / RND1 GTPase cycle / RND2 GTPase cycle / dendrite morphogenesis / efflux transmembrane transporter activity / PDZ domain binding / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / response to virus / late endosome / virus receptor activity / in utero embryonic development / protein-containing complex / membrane / plasma membrane / cytosol
Similarity search - Function
Kinase D-interacting substrate of 220 kDa-like, SAM domain-like / : / KAP family P-loop domain / KAP family P-loop domain / EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile. ...Kinase D-interacting substrate of 220 kDa-like, SAM domain-like / : / KAP family P-loop domain / KAP family P-loop domain / EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile. / Ankyrin repeats (many copies) / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Solute carrier family 53 member 1 / Kinase D-interacting substrate of 220 kDa
Similarity search - Component
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_61875.png

Downloads & links

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Map

FileDownload / File: emd_61875.map.gz / Format: CCP4 / Size: 329.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 441 pix.
= 465.255 Å		1.06 Å/pix.
x 442 pix.
= 466.31 Å		1.06 Å/pix.
x 443 pix.
= 467.365 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.7495336 - 2.4051201
Average (Standard dev.)0.004793993 (±0.02289209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-12-10-11
Dimensions442443441
Spacing443442441
CellA: 467.365 Å / B: 466.30997 Å / C: 465.25497 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of XPR1-KIDINS220

EntireName: Complex of XPR1-KIDINS220
Components
  • Complex: Complex of XPR1-KIDINS220
    • Protein or peptide: Kinase D-interacting substrate of 220 kDa
    • Protein or peptide: Solute carrier family 53 member 1

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Supramolecule #1: Complex of XPR1-KIDINS220

SupramoleculeName: Complex of XPR1-KIDINS220 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.823562 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 RAVRDISVAP LNADDQT LL EQMMDQDDGV RNR

UniProtKB: Solute carrier family 53 member 1

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Macromolecule #2: Kinase D-interacting substrate of 220 kDa

MacromoleculeName: Kinase D-interacting substrate of 220 kDa / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.367641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VDERNECGQT PLMIAAEQGN LEIVKELIKN GANCNLEDLD NWTALISASK EGHVHIVEEL LKCGVNLEHR DMGGWTALMW ACYKGRTDV VELLLSHGAN PSVTGLYSVY PIIWAAGRGH ADIVHLLLQN GAKVNCSDKY GTTPLVWAAR KGHLECVKHL L AMGADVDQ ...String:
VDERNECGQT PLMIAAEQGN LEIVKELIKN GANCNLEDLD NWTALISASK EGHVHIVEEL LKCGVNLEHR DMGGWTALMW ACYKGRTDV VELLLSHGAN PSVTGLYSVY PIIWAAGRGH ADIVHLLLQN GAKVNCSDKY GTTPLVWAAR KGHLECVKHL L AMGADVDQ EGANSMTALI VAVKGGYTQS VKEILKRNPN VNLTDKDGNT ALMIASKEGH TEIVQDLLDA GTYVNIPDRS GD TVLIGAV RGGHVEIVRA LLQKYADIDI RGQDNKTALY WAVEKGNATM VRDILQCNPD TEICTKDGET PLIKATKMRN IEV VELLLD KGAKVSAVDK KGDTPLHIAI RGRSRKLAEL LLRNPKDGRL LYRPNKAGET PYNIDCSHQK SILTQIFGAR

UniProtKB: Kinase D-interacting substrate of 220 kDa

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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 / Software - Name: cryoSPARC / Number images used: 295825
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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