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- PDB-9kmq: CryoEM structure of osPHT1-11 at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 9kmq
TitleCryoEM structure of osPHT1-11 at pH 8.0
ComponentsInorganic phosphate transporter 1-11
KeywordsTRANSPORT PROTEIN / phosphorus / rice / uptake
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 subsp. japonica (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDu, Z.M. / Guan, Z.Y. / Liu, Z.
Funding support China, 1items
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 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Inorganic phosphate transporter 1-11
A: Inorganic phosphate transporter 1-11


Theoretical massNumber of molelcules
Total (without water)127,1502
Polymers127,1502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Inorganic phosphate transporter 1-11 / OsPT11 / OsPht1 / 11 / H(+)/Pi cotransporter


Mass: 63575.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: PHT1-11, PT11, Os01g0657100, LOC_Os01g46860, OsJ_002785, P0694A04.21
Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q94DB8
Has protein modificationN

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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: osPHT1-11 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 346493 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036848
ELECTRON MICROSCOPYf_angle_d0.6659253
ELECTRON MICROSCOPYf_dihedral_angle_d4.417925
ELECTRON MICROSCOPYf_chiral_restr0.041043
ELECTRON MICROSCOPYf_plane_restr0.0031132

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