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- EMDB-61254: Closed structure of human XPR1 -

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Basic information

Entry
Database: EMDB / ID: EMD-61254
TitleClosed structure of human XPR1
Map data
Sample
  • Complex: human XPR1
    • Protein or peptide: Solute carrier family 53 member 1,Green fluorescent protein
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
  • Ligand: CHOLESTEROL
  • Ligand: PHOSPHATE ION
KeywordsXPR1 / Phosphate exporter / transporter / membrane protein / 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 / bioluminescence / generation of precursor metabolites and energy / response to virus ...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 / bioluminescence / generation of precursor metabolites and energy / 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. / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Solute carrier family 53 member 1
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang Y / Yang H / Shen H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2025
Title: Structural basis of phosphate export by human XPR1.
Authors: Yifei Wang / Yuechan Wang / Hui Yang / Ao Li / Dan Ma / Huaizong Shen /
History
DepositionAug 22, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61254.png

Downloads & links

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Map

FileDownload / File: emd_61254.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å		1.09 Å/pix.
x 256 pix.
= 278.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.738
Minimum - Maximum-5.0107718 - 7.7600775
Average (Standard dev.)0.0032891792 (±0.14154625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 278.272 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61254_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61254_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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,Green fluorescent protein
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
  • Ligand: CHOLESTEROL
  • 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,Green fluorescent protein

MacromoleculeName: Solute carrier family 53 member 1,Green fluorescent protein
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 112.31932 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 EANTGGRLEV LFQGPAAAAV SKGEELFT G VVPILVELDG DVNGHKFSVS GEGEGDATYG KLTLKFICTT GKLPVPWPTL VTTLTYGVQC FSRYPDHMKQ HDFFKSAMP EGYVQERTIF FKDDGNYTTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNYNSHN VYIMADKQKN GIKVNFKIRH NIEDGSVQL ADHYQQNTPI GDGPVLLPDN HYLSTQSKLS KDPNEKRDHM VLLEFVTAAG ITLGMDELYK SGLRSDYKDH D IDYKDDDD K

UniProtKB: Solute carrier family 53 member 1, Green fluorescent protein

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Macromolecule #2: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradeca...

MacromoleculeName: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
type: ligand / ID: 2 / Number of copies: 2 / Formula: 8PE
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-8PE:
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / phospholipid*YM

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 4 / Number of copies: 2 / 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

BufferpH: 7
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150104
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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