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- EMDB-18861: CryoEM structure of the asymmetric Pho90 dimer from yeast without... -

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Basic information

Entry
Database: EMDB / ID: EMD-18861
TitleCryoEM structure of the asymmetric Pho90 dimer from yeast without substrates.
Map data
Sample
  • Complex: Dimeric ScPho90
    • Protein or peptide: Low-affinity phosphate transporter PHO90
KeywordsPhosphate transporter / Plasma membrane protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of phosphate transmembrane transport / phosphate transmembrane transporter activity / phosphate ion transport / polyphosphate metabolic process / cell periphery / transmembrane transport / plasma membrane
Similarity search - Function
Citrate transporter-like domain / Citrate transporter / SPX domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
Low-affinity phosphate transporter PHO90
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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_18861.png

Downloads & links

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Map

FileDownload / File: emd_18861.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 448 pix.
= 256.704 Å		0.57 Å/pix.
x 448 pix.
= 256.704 Å		0.57 Å/pix.
x 448 pix.
= 256.704 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.573 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.269
Minimum - Maximum-0.69344306 - 1.3912114
Average (Standard dev.)0.005141953 (±0.038272824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 256.704 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_18861_additional_1.map
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Half map: #2

Fileemd_18861_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_18861_half_map_2.map
Projections & Slices
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Sample components

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Entire : Dimeric ScPho90

EntireName: Dimeric ScPho90
Components
  • Complex: Dimeric ScPho90
    • Protein or peptide: Low-affinity phosphate transporter PHO90

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Supramolecule #1: Dimeric ScPho90

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

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Macromolecule #1: Low-affinity phosphate transporter PHO90

MacromoleculeName: Low-affinity phosphate transporter PHO90 / 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: Low-affinity phosphate transporter PHO90

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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
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: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 33833
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 20 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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