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- EMDB-18859: CryoEM structure of the symmetric Pho90 dimer from yeast without ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18859
TitleCryoEM structure of the symmetric Pho90 dimer from yeast without substrates.
Map data
Sample
  • Complex: Dimeric ScPho90
    • Protein or peptide: PHO90 isoform 1
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: water
KeywordsPhosphate transporter / Plasma membrane protein / MEMBRANE PROTEIN
Function / homologyCitrate transporter-like domain / Citrate transporter / SPX domain / SPX domain / SPX domain profile. / transmembrane transporter activity / membrane / PHO90 isoform 1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsSchneider S / Kuehlbrandt W / Yildiz O
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Structure / Year: 2024
Title: Complementary structures of the yeast phosphate transporter Pho90 provide insights into its transport mechanism.
Authors: Simon Schneider / Werner Kühlbrandt / Özkan Yildiz /
Abstract: Phosphate homeostasis is essential for all living organisms. Low-affinity phosphate transporters are involved in phosphate import and regulation in a range of eukaryotic organisms. We have determined ...Phosphate homeostasis is essential for all living organisms. Low-affinity phosphate transporters are involved in phosphate import and regulation in a range of eukaryotic organisms. We have determined the structures of the Saccharomyces cerevisiae phosphate importer Pho90 by electron cryomicroscopy in two complementary states at 2.3 and 3.1 Å resolution. The symmetrical, outward-open structure in the presence of phosphate indicates bound substrate ions in the binding pocket. In the absence of phosphate, Pho90 assumes an asymmetric structure with one monomer facing inward and one monomer facing outward, providing insights into the transport mechanism. The Pho90 transport domain binds phosphate ions on one side of the membrane, then flips to the other side where the substrate is released. Together with functional experiments, these complementary structures illustrate the transport mechanism of eukaryotic low-affinity phosphate transporters.
History
DepositionNov 8, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18859.png

Downloads & links

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Map

FileDownload / File: emd_18859.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 512 pix.
= 293.376 Å		0.57 Å/pix.
x 512 pix.
= 293.376 Å		0.57 Å/pix.
x 512 pix.
= 293.376 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.573 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.566
Minimum - Maximum-1.4022979 - 2.2172844
Average (Standard dev.)0.00022588678 (±0.04294966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 293.376 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_18859_additional_1.map
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Additional map: #1

Fileemd_18859_additional_2.map
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Half map: #2

Fileemd_18859_half_map_1.map
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Half map: #1

Fileemd_18859_half_map_2.map
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Sample components

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Entire : Dimeric ScPho90

EntireName: Dimeric ScPho90
Components
  • Complex: Dimeric ScPho90
    • Protein or peptide: PHO90 isoform 1
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: water

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Supramolecule #1: Dimeric ScPho90

SupramoleculeName: Dimeric ScPho90 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: PHO90 isoform 1

MacromoleculeName: PHO90 isoform 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 97.786219 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MRFSHFLKYN AVPEWQNHYM DYSELKNLIY TLQTDELQVG DNEEGFGAGK SSNITDRFKN KFSFKNAKED TSSGMNKDAG IVEETIELR ELPTAQTVAA KPSPFRRMKE KIFYKRRSSS ASSVSSTANE NLQLDTYDTF VGDLTAEKQK VDDFYKRTEA K FYDKFDAL ...String:
MRFSHFLKYN AVPEWQNHYM DYSELKNLIY TLQTDELQVG DNEEGFGAGK SSNITDRFKN KFSFKNAKED TSSGMNKDAG IVEETIELR ELPTAQTVAA KPSPFRRMKE KIFYKRRSSS ASSVSSTANE NLQLDTYDTF VGDLTAEKQK VDDFYKRTEA K FYDKFDAL VKDLKKIGVI EYDIDDDTLF NEPIASTNDE VPPLDLDDDE DDDEFYDDQS NIEDNTALLH HSQYNIKSQK KS LLKKSIV NLYIDLCQLK SFIELNRIGF AKITKKSDKV LHLNTRTELI ESEQFFKDTY AFQAETIELL NSKISQLVTF YAR ITDRPH NISHSKQELK SYLHDHIVWE RSNTWKDMLG LLSQADELTP KETEYNANKL VGKLDLEYYR WPLPRPINLK FTSI NNVAL PKLFFTKKAY KIYFIILVTG LLLGIKTFND AAQHRCMALV ECVAFLWASE AIPLHITAFL VPLLVVLFKV LKTSD GAIM SAASASSEIL AAMWSSTIMI LLAGFTLGEV LAQYNIAKVL ASWLLAFAGC KPRNVLLMAM CVVFFLSMWI SNVAAP VLT YSLLSPLLDA MDADSPFAQA LVLGVALAAN IGGMSSPISS PQNIISMSYL KPYGIGWGQF FAVALPSGIL AMLLVWI LL FTTFKMNKTK LEKFKPIKTK FTVKQYYIIT VTVATILLWC VESQIEGAFG SSGQIAIIPI VLFFGTGLLS TQDLNAFP W SIVILAMGGI ALGKAVSSSG LLSTIAKALQ KKIENDGVFA ILCIFGILML VVGTFVSHTV SAIIIIPLVQ EVGDKLGNP KAAPILVFGC ALLSSCGMGL ASSGFPNVTA ISKVDRKGDR YLSVMTFLTR GVPASILAFL CVITLGYGIM ASVVKGNATS A

UniProtKB: PHO90 isoform 1

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Macromolecule #2: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 328 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration4.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
20.0 mMTris
GridMaterial: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 304932
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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