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- PDB-9ik4: Cryo-EM structure of Arabidopsis thaliana phosphate transporter P... -

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Basic information

Entry
Database: PDB / ID: 9ik4
TitleCryo-EM structure of Arabidopsis thaliana phosphate transporter PHO1;H1
ComponentsPhosphate transporter PHO1 homolog 1
KeywordsMEMBRANE PROTEIN / phosphate transport / SPX domain / SPX-EXS / InsP6 / PHO1
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
INOSITOL HEXAKISPHOSPHATE / PHOSPHATE ION / Phosphate transporter PHO1 homolog 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsFang, S. / Zhang, X. / Zhang, P.
Funding support China, 1items
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
DepositionJun 26, 2024Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate transporter PHO1 homolog 1
B: Phosphate transporter PHO1 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,3156
Polymers178,8052
Non-polymers1,5104
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Phosphate transporter PHO1 homolog 1 / Protein PHO1 homolog 1 / AtPHO1 / H1


Mass: 89402.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PHO1-H1, At1g68740, F14K14.15, F24J5.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q93ZF5
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Phosphate transporter PHO1;H1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 20000 nm / Nominal defocus min: 8000 nm
Image recordingElectron dose: 58.5 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.14_3260: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 375307 / Symmetry type: POINT

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