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- EMDB-61140: CryoEM structure of human XPR1 in complex with phosphate in state B -

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Basic information

Entry
Database: EMDB / ID: EMD-61140
TitleCryoEM structure of human XPR1 in complex with phosphate in state B
Map data
Sample
  • Complex: Human XPR1
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PHOSPHATE ION
KeywordsPhosphate / Transport / XPR1 / 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: 3.1 Å
AuthorsZhang WH / Chen YK / Guan ZY / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the mechanism of phosphate recognition and transport by XPR1.
Authors: Wenhui Zhang / Yanke Chen / Zeyuan Guan / Yong Wang / Meng Tang / Zhangmeng Du / Jie Zhang / Meng Cheng / Jiaqi Zuo / Yan Liu / Qiang Wang / Yanjun Liu / Delin Zhang / Ping Yin / Ling Ma / Zhu Liu /
Abstract: XPR1 is the sole protein known to transport inorganic phosphate (Pi) out of cells, a function conserved across species from yeast to mammals. Human XPR1 variants lead to cerebral calcium-phosphate ...XPR1 is the sole protein known to transport inorganic phosphate (Pi) out of cells, a function conserved across species from yeast to mammals. Human XPR1 variants lead to cerebral calcium-phosphate deposition and primary familial brain calcification (PFBC), a hereditary neurodegenerative disorder. Here, we present the cryo-EM structure of human XPR1 in both its Pi-unbound and various Pi-bound states. XPR1 features 10 transmembrane α-helices forming an ion channel-like structure, with multiple Pi recognition sites along the channel. Pathogenic mutations in two arginine residues, which line the translocation channel, disrupt Pi transport. Molecular dynamics simulations reveal that Pi ion undergoes a stepwise transition through the sequential recognition sites during the transport process. Together with functional analyses, our results suggest that this sequential arrangement allows XPR1 to facilitate Pi ion passage via a "relay" process, and they establish a framework for the interpretation of disease-related mutations and for the development of future therapeutics.
History
DepositionAug 11, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61140.png

Downloads & links

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Map

FileDownload / File: emd_61140.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.671377 - 3.9987159
Average (Standard dev.)-0.001066301 (±0.06955733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61140_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61140_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Human XPR1

EntireName: Human XPR1
Components
  • Complex: Human XPR1
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Human XPR1

SupramoleculeName: Human 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.595844 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 RNRQKNRSWK YNQSISLRRP RLASQSKARD TKVLIEDTDD EANTLEDYKD HDGDYKDHDI DYKDDDDK

UniProtKB: Solute carrier family 53 member 1

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Macromolecule #2: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / Number of copies: 1 / 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

Concentration4.7 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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