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- PDB-23ic: Cryo-EM structure of Oryza sativa vacuolar phosphate efflux trans... -

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Basic information

Entry
Database: PDB / ID: 23ic
TitleCryo-EM structure of Oryza sativa vacuolar phosphate efflux transporter 2 (OsVPE2)
ComponentsOs08g0156600 protein
KeywordsTRANSPORT PROTEIN / vacuolar phosphate efflux transporter / Monomer
Function / homology:
Function and homology information
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLiu, Z. / Cao, S. / Zou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32422041 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Decoding plant vacuolar phosphate efflux: Structural and dynamic insights from rice VPE2.
Authors: Jiaqi Zuo / Shuo Cao / Ying Tang / Haitao He / Jie Zhang / Peiru Li / Yanke Chen / Ping Yin / Chuang Wang / Lizhong Xiong / Faming Dong / Zhu Liu /
Abstract: Vacuoles store up to 90% of cellular phosphorus in plants, serving as a critical buffer against cytosolic fluctuations during environmental nutrient stress. Despite this central role, the molecular ...Vacuoles store up to 90% of cellular phosphorus in plants, serving as a critical buffer against cytosolic fluctuations during environmental nutrient stress. Despite this central role, the molecular mechanisms governing vacuolar inorganic phosphate (Pi) release through vacuolar Pi efflux transporters (VPEs) remain unclear. Through integrative structural biology, we elucidate how the rice transporter OsVPE2 transports Pi out of vacuoles. Cryoelectron microscopy structures capture distinct functional states, revealing a Pi-binding pocket and a unique vacuolar coupling helix (VCH) motif that undergoes pH-dependent conformational switching. Single-molecule fluorescence resonance energy transfer analyses reveal the intrinsic dynamics of the VCH, demonstrating that its movement is coupled with the transporter's conformational changes. This dynamic VCH functions as a conformational switch, regulating the transporter cycle: its embedding into the transmembrane vestibule stabilizes transporter's outward-occluded state, while its displacement enables the transition to the inward-open conformation. Functional studies demonstrate that VCH flexibility-not mere presence-is essential for transport, and its disruption impairs function. Our work establishes the molecular blueprint for vacuolar Pi efflux, identifying this evolutionarily conserved regulatory VCH among VPEs as a potential target for structure-guided engineering to optimize plant phosphorus recycling and use efficiency.
History
DepositionFeb 6, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Os08g0156600 protein


Theoretical massNumber of molelcules
Total (without water)53,7101
Polymers53,7101
Non-polymers00
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 Os08g0156600 protein


Mass: 53710.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os08g0156600 / Production host: Homo (humans) / References: UniProt: A0A0P0XCF9
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: O. sativa vacuolar phosphate efflux transporter 2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Oryza sativa Japonica Group (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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155111 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033323
ELECTRON MICROSCOPYf_angle_d0.6414526
ELECTRON MICROSCOPYf_dihedral_angle_d3.778445
ELECTRON MICROSCOPYf_chiral_restr0.043528
ELECTRON MICROSCOPYf_plane_restr0.005547

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