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- EMDB-65525: Cryo-EM structure of a Fungal XPR1 with InsP6 -

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Basic information

Entry
Database: EMDB / ID: EMD-65525
TitleCryo-EM structure of a Fungal XPR1 with InsP6
Map data
Sample
  • Complex: SpXPR1 with InsP6
    • Protein or peptide: Protein SYG1 homolog
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: PHOSPHATE ION
Keywordsphosphate exporter / dimer / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


phosphate ion export across plasma membrane / phosphate transmembrane transporter activity / phosphate ion transport / cellular response to phosphate starvation / inositol hexakisphosphate binding / plasma membrane
Similarity search - Function
EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
Phosphate exporter spx2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) / Schizosaccharomyces pombe 972h- (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsShen HZ / Yang H / Wang YC
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2024YFA0916903 China
CitationJournal: To Be Published
Title: Structural insights into the gating mechanism of a fission yeast phosphate exporter SpXpr1
Authors: Shen HZ / Yang H / Wang YC
History
DepositionJul 25, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65525.png

Downloads & links

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Map

FileDownload / File: emd_65525.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 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: 0.782
Minimum - Maximum-3.1530635 - 5.727275
Average (Standard dev.)-0.0016196128 (±0.07829868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 391.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65525_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_65525_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 : SpXPR1 with InsP6

EntireName: SpXPR1 with InsP6
Components
  • Complex: SpXPR1 with InsP6
    • Protein or peptide: Protein SYG1 homolog
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: PHOSPHATE ION

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Supramolecule #1: SpXPR1 with InsP6

SupramoleculeName: SpXPR1 with InsP6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)

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Macromolecule #1: Protein SYG1 homolog

MacromoleculeName: Protein SYG1 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972
Molecular weightTheoretical: 82.913281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG GSGSGGSGSG SSGSTGKFGK VIEGQSVAEW ASAYFDYKKG KKIIAGIAKN PSEGLYGTSG ILGETPEEAI VKRGQIHRF HPLFQEFLDQ QANKVEEFFE NLVSDARERM DLISDQVDIY EKLRAFKKGT LESGSVVLIQ KQHSKLRQRL D SILNFSRL ...String:
MDYKDDDDKG GSGSGGSGSG SSGSTGKFGK VIEGQSVAEW ASAYFDYKKG KKIIAGIAKN PSEGLYGTSG ILGETPEEAI VKRGQIHRF HPLFQEFLDQ QANKVEEFFE NLVSDARERM DLISDQVDIY EKLRAFKKGT LESGSVVLIQ KQHSKLRQRL D SILNFSRL QPAYHIPARK SVPTDAYTPM VSYRKLKSKL KTTLLDFYDY LKLVSQYQHL NQQAFRKIVK KYDKTLHTDL QG FWVDYMS RYTFTDFSIT TNWQLHVEDI YARLFTNHNK KLALEHLKSF RQKEHFSANS MRFGLLFGAG LPLAIEAACY YNA TEQSSY LLQIWGGFFL VIFAFVLFDL DCYVWEKTRV NYMLIFEFNQ RKSLNWRQHL EIVGAVFFIF SLFFFLCMRN FFPG FTIYF PALFLGVVGT FLIAPVIVPY WRMRRYLIIQ LIRVFLSGLS TVHFQDFFFA DQMVSLTYAC GNISLFFCLY KRLWR QPQL CNSSHSPLLG FFTTLPGILR VFQCFRRYSD SLKSFPHLVN ALKYIFNILA QMFLSLWRIH PGLKYRVLYT IFAGVN SLF SYTWDILMDW NLLVRKDGRW QFREHRILKQ LWPYIIAMIL NFIVRSSFIF YCIFPNHIQH SSGISFFVTL AEIMRRC MW NILRVEHEEI YNRENLRAAR ELKPLDFVKP HSDVFVSHQI SSDKNYTDDE DSMDDQTDVD EAQFS

UniProtKB: Phosphate exporter spx2

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 18 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #3: (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: 3 / 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 #4: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 6 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 226844
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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