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- EMDB-62480: CryoEM structure of osPHT1-11 at pH 5.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-62480
TitleCryoEM structure of osPHT1-11 at pH 5.0
Map data
Sample
  • Complex: osPHT1-11
    • Protein or peptide: Inorganic phosphate transporter 1-11
  • Ligand: PHOSPHATE ION
Keywordsphosphorus / rice / uptake / TRANSPORT PROTEIN
Function / homology
Function and homology information


phosphate transmembrane transporter activity / phosphate ion transport / symporter activity / membrane
Similarity search - Function
Phosphate permease / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Inorganic phosphate transporter 1-11
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDu ZM / Guan ZY / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Dev Cell / Year: 2025
Title: Cryo-EM structure and dynamic basis of phosphate uptake by PHT1 in rice.
Authors: Zhangmeng Du / Zeyuan Guan / Hai Liu / Jie Zhang / Haitao He / Zhiwen Zheng / Wenhui Zhang / Lihuan Jiang / Jiaqi Zuo / Yan Liu / Beijing Wan / Haifu Tu / Faming Dong / Xuelei Lai / Lizhong ...Authors: Zhangmeng Du / Zeyuan Guan / Hai Liu / Jie Zhang / Haitao He / Zhiwen Zheng / Wenhui Zhang / Lihuan Jiang / Jiaqi Zuo / Yan Liu / Beijing Wan / Haifu Tu / Faming Dong / Xuelei Lai / Lizhong Xiong / Ping Yin / Shaowu Xue / Yanke Chen / Zhu Liu /
Abstract: Phosphorus is an essential macronutrient for plants, primarily absorbed from the soil as inorganic phosphate (Pi) through root-located Pi transporters. Despite decades of research into these ...Phosphorus is an essential macronutrient for plants, primarily absorbed from the soil as inorganic phosphate (Pi) through root-located Pi transporters. Despite decades of research into these transporters as targets for developing Pi-efficient crops, their mechanisms for Pi import remain poorly understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of the rice Pi importer OsPHT1;11 in both Pi-bound and unbound forms, characterize its conformational dynamics, and demonstrate how these dynamics contribute to its transport function. Pi is recognized through conserved residues found in plants, with its translocation facilitated by a typical alternating-access mechanism. Single-molecule fluorescence resonance energy transfer (smFRET) analyses show that this transporter undergoes dynamic conformational fluctuations, which are differentially linked to its Pi transport capability, with a predominance of extracellular open conformations favoring Pi transport, while more populated intracellular open conformations hinder it. These findings highlight key conformational determinants of transport activity and provide mechanistic insights into Pi uptake in plants.
History
DepositionNov 21, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62480.png

Downloads & links

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Map

FileDownload / File: emd_62480.map.gz / Format: CCP4 / Size: 83.7 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.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.0234997 - 2.7565024
Average (Standard dev.)-0.000030162288 (±0.056732524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62480_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62480_half_map_2.map
Projections & Slices
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Sample components

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Entire : osPHT1-11

EntireName: osPHT1-11
Components
  • Complex: osPHT1-11
    • Protein or peptide: Inorganic phosphate transporter 1-11
  • Ligand: PHOSPHATE ION

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Supramolecule #1: osPHT1-11

SupramoleculeName: osPHT1-11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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Macromolecule #1: Inorganic phosphate transporter 1-11

MacromoleculeName: Inorganic phosphate transporter 1-11 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 63.575168 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG DYKDDDDKID YKDDDDKGSM ADADGGSNLA VLDALDSART QMYHMKAIVI AGMGFFTDAY DLFCISTVSK LLGRLYYQP DGSTDSKPGA LSKTANNMVI GVALVGTLMG QLVFGYFGDK LGRKRVYGVT LILMAACAIG SGLSFGSSRK A VIGTLCFF ...String:
MDYKDDDDKG DYKDDDDKID YKDDDDKGSM ADADGGSNLA VLDALDSART QMYHMKAIVI AGMGFFTDAY DLFCISTVSK LLGRLYYQP DGSTDSKPGA LSKTANNMVI GVALVGTLMG QLVFGYFGDK LGRKRVYGVT LILMAACAIG SGLSFGSSRK A VIGTLCFF RFWLGFGIGG DYPLSATIMS EYSNKKTRGA FIAAVFAMQG VGIIFAGLVS MIVSSIFLTY NKAPSYKGNH DL SRQMPAA DYVWRIVLMI GAFPALATFY WRMKMPETAR YTAIIDGNAK QAANDMQKVL SIEIEAEQEK LAKFNAANNY PLL SMEFAR RHGLHLIGTT TTWFLLDIAF YSQNLTQKDI FPAMGLISGA AEVNALTEMF QISKASFLVA LLGTFPGYWV TVAL IDKMG RYMIQLIGFF MMSMFMLAMG ILYDYLKTHH FLFGLLYALT FFFANFGPNS TTFVLPAELF PTRVRSTCHA ISAAA GKAG AIVAAFGIQK LTYNSQVKSI KKALIILSIT NMLGFFFTFL VPETMGRSLE EISGEDGNTG AGGGGAPAAA NAGVGV SAS DVSRDEKFPA SSTEWQTSMH A

UniProtKB: Inorganic phosphate transporter 1-11

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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: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 333051
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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