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- EMDB-62621: Cryo-EM structure of the human XPR1 with spx domain -

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Basic information

Entry
Database: EMDB / ID: EMD-62621
TitleCryo-EM structure of the human XPR1 with spx domain
Map data
Sample
  • Complex: The structure of Human XPR1 with SPX domain
KeywordsSLC transporter / XPR1 / SLC53A1 / structural protein / Pi / exporter
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsShe J / Chen L
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0600800 China
National Natural Science Foundation of China (NSFC)32071201 China
National Natural Science Foundation of China (NSFC)32100967 China
CitationJournal: Nat Commun / Year: 2025
Title: Structure and function of human XPR1 in phosphate export.
Authors: Long Chen / Jin He / Mingxing Wang / Ji She /
Abstract: Xenotropic and polytropic retrovirus receptor 1 (XPR1) functions as a phosphate exporter and is pivotal in maintaining human phosphate homeostasis. It has been identified as a causative gene for ...Xenotropic and polytropic retrovirus receptor 1 (XPR1) functions as a phosphate exporter and is pivotal in maintaining human phosphate homeostasis. It has been identified as a causative gene for primary familial brain calcification. Here we present the cryogenic electron microscopy (cryo-EM) structure of human XPR1 (HsXPR1). HsXPR1 exhibits a dimeric structure in which only TM1 directly constitutes the dimer interface of the transmembrane domain. Each HsXPR1 subunit can be divided spatially into a core domain and a scaffold domain. The core domain of HsXPR1 forms a pore-like structure, along which two phosphate-binding sites enriched with positively charged residues are identified. Mutations of key residues at either site substantially diminish the transport activity of HsXPR1. Phosphate binding at the central site may trigger a conformational change at TM9, leading to the opening of the extracellular gate. In addition, our structural analysis reveals a new conformational state of HsXPR1 in which the cytoplasmic SPX domains form a V-shaped structure. Altogether, our results elucidate the overall architecture of HsXPR1 and shed light on XPR1-mediated phosphate export.
History
DepositionDec 6, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62621.png

Downloads & links

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Map

FileDownload / File: emd_62621.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å		0.82 Å/pix.
x 320 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0043
Minimum - Maximum-0.0064243767 - 0.012357488
Average (Standard dev.)0.000030850835 (±0.0006460317)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The structure of Human XPR1 with SPX domain

EntireName: The structure of Human XPR1 with SPX domain
Components
  • Complex: The structure of Human XPR1 with SPX domain

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Supramolecule #1: The structure of Human XPR1 with SPX domain

SupramoleculeName: The structure of Human XPR1 with SPX domain / type: complex / ID: 1 / Parent: 0
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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 345317
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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