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- EMDB-61430: Cryo-EM structure of the EXS domain of Arabidopsis thaliana phosp... -

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Basic information

Entry
Database: EMDB / ID: EMD-61430
TitleCryo-EM structure of the EXS domain of Arabidopsis thaliana phosphatetransporter PHO1;H1
Map data
Sample
  • Complex: EXS domain of Arabidopsis PHO1;H1
    • Protein or peptide: Phosphate transporter PHO1 homolog 1
  • Ligand: PHOSPHATE ION
Keywordsphosphate transport / SPX domain / PHO1 / SPX-EXS / cryo-EM / InsP6 / MEMBRANE PROTEIN
Function / homology
Function and homology information


phosphate ion transport / cellular response to phosphate starvation / plasma membrane
Similarity search - Function
PHO1, SPX domain / : / EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
Phosphate transporter PHO1 homolog 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsFang S / Zhang X / Zhang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Plants / Year: 2025
Title: Structural mechanism underlying PHO1;H1-mediated phosphate transport in Arabidopsis.
Authors: Sunzhenhe Fang / Yang Yang / Xue Zhang / Zhao Yang / Minhua Zhang / Yang Zhao / Chensi Zhang / Fang Yu / Yong-Fei Wang / Peng Zhang /
Abstract: Arabidopsis PHOSPHATE 1 (AtPHO1) and its closest homologue AtPHO1;H1 are phosphate transporters that load phosphate into the xylem vessel for root-to-shoot translocation. AtPHO1 and AtPHO1;H1 are ...Arabidopsis PHOSPHATE 1 (AtPHO1) and its closest homologue AtPHO1;H1 are phosphate transporters that load phosphate into the xylem vessel for root-to-shoot translocation. AtPHO1 and AtPHO1;H1 are prototypical members of the unique SPX-EXS family, whose structural and molecular mechanisms remain elusive. In this study, we determined the cryogenic electron microscopy structure of AtPHO1;H1 binding with inorganic phosphate (Pi) and inositol hexakisphosphate in a closed conformation. Further molecular dynamic simulation and AlphaFold prediction support an open conformation. AtPHO1;H1 forms a domain-swapped homodimer that involves both the transmembrane ERD1/XPR1/SYG1 (EXS) domain and the cytoplasmic SYG1/Pho81/XPR1 (SPX) domain. The EXS domain presented by the SPX-EXS family represents a novel protein fold, and an independent substrate transport pathway and substrate-binding site are present in each EXS domain. Two gating residues, Trp719 and Tyr610, are identified above the substrate-binding site to control opening and closing of the pathway. The SPX domain features positively charged patches and/or residues at the dimer interface to accommodate inositol hexakisphosphate molecules, whose binding mediates dimerization and enhances AtPHO1;H1 activity. In addition, a C-terminal tail is required for AtPHO1;H1 activity. On the basis of structural and functional analysis, a working model for Pi efflux mediated by AtPHO1;H1 and its homologues was postulated, suggesting a channel-like mechanism. This study not only reveals the molecular and regulatory mechanism underlying Pi transport mediated by the unique SPX-EXS family, but also provides potential for crop engineering to enhance phosphorus-use efficiency in sustainable agriculture.
History
DepositionSep 4, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61430.png

Downloads & links

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Map

FileDownload / File: emd_61430.map.gz / Format: CCP4 / Size: 113.6 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.)
0.83 Å/pix.
x 310 pix.
= 257.3 Å		0.83 Å/pix.
x 310 pix.
= 257.3 Å		0.83 Å/pix.
x 310 pix.
= 257.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.868014 - 4.26649
Average (Standard dev.)-0.0023131636 (±0.074871704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 257.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_61430_additional_1.map
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Half map: #1

Fileemd_61430_half_map_1.map
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Half map: #2

Fileemd_61430_half_map_2.map
Projections & Slices
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Sample components

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Entire : EXS domain of Arabidopsis PHO1;H1

EntireName: EXS domain of Arabidopsis PHO1;H1
Components
  • Complex: EXS domain of Arabidopsis PHO1;H1
    • Protein or peptide: Phosphate transporter PHO1 homolog 1
  • Ligand: PHOSPHATE ION

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Supramolecule #1: EXS domain of Arabidopsis PHO1;H1

SupramoleculeName: EXS domain of Arabidopsis PHO1;H1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Phosphate transporter PHO1 homolog 1

MacromoleculeName: Phosphate transporter PHO1 homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 90.830117 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVKFTKQFEG QLVPEWKDAF VDYSQLKKDL KKIHLFTNGV EKKHTETSLI KTVKSSLGRL SIFGNKGREQ SRVIQVHKKL ASSGSNNDV YETELLEKIA DDTDAAKEFF ACLDMQLNKV NQFYKTKEKE FLERGECLKK QMDILIELKD AFKQKQANGE S TQESKEDD ...String:
MVKFTKQFEG QLVPEWKDAF VDYSQLKKDL KKIHLFTNGV EKKHTETSLI KTVKSSLGRL SIFGNKGREQ SRVIQVHKKL ASSGSNNDV YETELLEKIA DDTDAAKEFF ACLDMQLNKV NQFYKTKEKE FLERGECLKK QMDILIELKD AFKQKQANGE S TQESKEDD SISCTISCEY DSVRGRTEEM QLQVSCLDNL EDNGEEALES LGSEEPIKAN NEDSKLTTVS SRVFSCQGKN VK IKIPLTN PSRTFSAISY LINQSSSKKN GPDGGNKLQI SKKKLSHAEK MIKGALTELF KGLNYLKTYR NLNILAFMNI LKK FDKVTG KQILPIYLKV VESSYFNISD KVMILSDEVE EWFIKHLAGE NRRKAMKYLK PHHRKESHSV TFFIGLFTGC FVAL LAGYI IVAHLTGMYR QHSANTFYME TAYPVLSMFG LLFLHLFLYG CNIFMWRKAR INYSFIFELG SKNELKYRDV FLICT ASMS AIAGVMFVHL SLLEKGYSFR QVQVIPGLLL LGFLLILICP LNIFYKSSRY RLISVIRNIV FSPLYKVVML DFFMAD QLC SQVPMLRNLE YIACYYITGS YATQDYEYCM RVKYYRDLAY AVSFLPYYWR AMQCARRWFD EGETSHLVNL GKYVSAM LA AGTKVAYEKE RSLGWLCLVV AMSSVATIYQ LYWDFVKDWG LLQHNSNNPW LRNQLMLRQK SIYYFSMVLN LVLRLAWL Q TVLHSSFEHV DYRVTGLFLA ALEVIRRGQW NFYRLENEHL NNAGKFRAVK TVPLPFREVD EED

UniProtKB: Phosphate transporter PHO1 homolog 1

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Macromolecule #2: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 2 / Number of copies: 1 / 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 288715
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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