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- EMDB-39210: Cryo EM structure of human phosphate channel XPR1 at open and inw... -

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Basic information

Entry
Database: EMDB / ID: EMD-39210
TitleCryo EM structure of human phosphate channel XPR1 at open and inward-facing state
Map data
Sample
  • Complex: Cryo EM structure of human phosphate channel XPR1 at open and inward-facing state
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordsphosphate channel / membrane protein / phosphate homeostasis / 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: 3.41 Å
AuthorsLu Y / Yue C / Zhang L / Yao D / Yu Y / Cao Y
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072468 China
National Natural Science Foundation of China (NSFC)82272519 China
National Natural Science Foundation of China (NSFC)32371289 China
National Natural Science Foundation of China (NSFC)82072468 China
CitationJournal: Science / Year: 2024
Title: Structural basis for inositol pyrophosphate gating of the phosphate channel XPR1.
Authors: Yi Lu / Chen-Xi Yue / Li Zhang / Deqiang Yao / Ying Xia / Qing Zhang / Xinchen Zhang / Shaobai Li / Yafeng Shen / Mi Cao / Chang-Run Guo / An Qin / Jie Zhao / Lu Zhou / Ye Yu / Yu Cao /
Abstract: Precise regulation of intracellular phosphate (Pi) is critical for cellular function, with xenotropic and polytropic retrovirus receptor 1 (XPR1) serving as the sole Pi exporter in humans. The ...Precise regulation of intracellular phosphate (Pi) is critical for cellular function, with xenotropic and polytropic retrovirus receptor 1 (XPR1) serving as the sole Pi exporter in humans. The mechanism of Pi efflux, activated by inositol pyrophosphates (PP-IPs), has remained unclear. This study presents cryo-electron microscopy structures of XPR1 in multiple conformations, revealing a transmembrane pathway for Pi export and a dual-binding activation pattern for PP-IPs. A canonical binding site is located at the dimeric interface of Syg1/Pho81/XPR1 (SPX) domains, and a second site, biased toward PP-IPs, is found between the transmembrane and SPX domains. By integrating structural studies with electrophysiological analyses, we characterized XPR1 as an inositol phosphates (IPs)/PP-IPs-activated phosphate channel. The interplay among its transmembrane domains, SPX domains, and IPs/PP-IPs orchestrates the conformational transition between its closed and open states.
History
DepositionFeb 24, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39210.png

Downloads & links

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Map

FileDownload / File: emd_39210.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.7163115 - 5.447511
Average (Standard dev.)-0.0011649677 (±0.10337304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39210_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_39210_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo EM structure of human phosphate channel XPR1 at open and inw...

EntireName: Cryo EM structure of human phosphate channel XPR1 at open and inward-facing state
Components
  • Complex: Cryo EM structure of human phosphate channel XPR1 at open and inward-facing state
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Cryo EM structure of human phosphate channel XPR1 at open and inw...

SupramoleculeName: Cryo EM structure of human phosphate channel XPR1 at open and inward-facing state
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: 46.179883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QPAPAWTTFR VGLFCGIFIV LNITLVLAAV FKLETDRSIW PLIRIYRGGF LLIEFLFLLG INTYGWRQAG VNHVLIFELN PRSNLSHQH LFEIAGFLGI LWCLSLLACF FAPISVIPTY VYPLALYGFM VFFLINPTKT FYYKSRFWLL KLLFRVFTAP F HKVGFADF ...String:
QPAPAWTTFR VGLFCGIFIV LNITLVLAAV FKLETDRSIW PLIRIYRGGF LLIEFLFLLG INTYGWRQAG VNHVLIFELN PRSNLSHQH LFEIAGFLGI LWCLSLLACF FAPISVIPTY VYPLALYGFM VFFLINPTKT FYYKSRFWLL KLLFRVFTAP F HKVGFADF WLADQLNSLS VILMDLEYMI CFYSLELKWD ESKGLLPNNS EESGICHKYT YGVRAIVQCI PAWLRFIQCL RR YRDTKRA FPHLVNAGKY STTFFMVTFA ALYSTHKERG HSDTMVFFYL WIVFYIISSC YTLIWDLKMD WGLFDKNAGE NTF LREEIV YPQKAYYYCA IIEDVILRFA WTIQISITST TLLPHSGDII ATVFAPLEVF RRFVWNFFRL ENEHLNN

UniProtKB: Solute carrier family 53 member 1

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 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: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 447733
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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