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- EMDB-39230: Cryo EM structure of human phosphate channel XPR1 at intermediate... -

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Basic information

Entry
Database: EMDB / ID: EMD-39230
TitleCryo EM structure of human phosphate channel XPR1 at intermediate state
Map data
Sample
  • Complex: Cryo EM structure of human phosphate channel XPR1 at intermediate state
    • Protein or peptide: Solute carrier family 53 member 1
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 / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / virus receptor activity / Golgi apparatus ...phosphate transmembrane transporter activity / phosphate ion transport / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / virus receptor activity / Golgi apparatus / plasma membrane / cytoplasm
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: 4.59 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 XPR1 serving as the sole Pi exporter in humans. The mechanism of Pi efflux, activated by inositol ...Precise regulation of intracellular phosphate (Pi) is critical for cellular function, with 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 by PP-IPs. A canonical binding site is located at the dimeric interface of 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 characterize XPR1 as an IPs/PP-IPs-activated phosphate channel. The interplay among its TMDs, SPX domains, and IPs/PP-IPs orchestrates the conformational transition between its closed and open states.
History
DepositionFeb 25, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39230.png

Downloads & links

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Map

FileDownload / File: emd_39230.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3326489 - 1.8593566
Average (Standard dev.)-0.0013626567 (±0.04132378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39230_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_39230_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 intermediate...

EntireName: Cryo EM structure of human phosphate channel XPR1 at intermediate state
Components
  • Complex: Cryo EM structure of human phosphate channel XPR1 at intermediate state
    • Protein or peptide: Solute carrier family 53 member 1

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Supramolecule #1: Cryo EM structure of human phosphate channel XPR1 at intermediate...

SupramoleculeName: Cryo EM structure of human phosphate channel XPR1 at intermediate state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 70.388328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QYEAFKDMLY SAQDQAPSVE VTDEDTVKRY FAKFEEKFFQ TCEKELAKIN TFYSEKLAEA QRRFATLQNE LQSSLDAQKE STGVTTLRQ RRKPVFHLSH EERVQHRNIK DLKLAFSEFY LSLILLQNYQ NLNFTGFRKI LKKHDKILET SRGADWRVAH V EVAPFYTC ...String:
QYEAFKDMLY SAQDQAPSVE VTDEDTVKRY FAKFEEKFFQ TCEKELAKIN TFYSEKLAEA QRRFATLQNE LQSSLDAQKE STGVTTLRQ RRKPVFHLSH EERVQHRNIK DLKLAFSEFY LSLILLQNYQ NLNFTGFRKI LKKHDKILET SRGADWRVAH V EVAPFYTC KKINQLISET EAVVTNELED GDRQKAMKRL RVPPLGAAQP APAWTTFRVG LFCGIFIVLN ITLVLAAVFK LE TDRSIWP LIRIYRGGFL LIEFLFLLGI NTYGWRQAGV NHVLIFELNP RSNLSHQHLF EIAGFLGILW CLSLLACFFA PIS VIPTYV YPLALYGFMV FFLINPTKTF YYKSRFWLLK LLFRVFTAPF HKVGFADFWL ADQLNSLSVI LMDLEYMICF YSLE LKWDE SKGLLPNNSE ESGICHKYTY GVRAIVQCIP AWLRFIQCLR RYRDTKRAFP HLVNAGKYST TFFMVTFAAL YSTHK ERGH SDTMVFFYLW IVFYIISSCY TLIWDLKMDW GLFDKNAGEN TFLREEIVYP QKAYYYCAII EDVILRFAWT IQISIT STT LLPHSGDIIA TVFAPLEVFR RFVWNFFRLE NEHLNNC

UniProtKB: Solute carrier family 53 member 1

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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: 4.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111129
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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