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- EMDB-68992: Cryo-EM structure of Oryza sativa vacuolar phosphate efflux trans... -

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Basic information

Entry
Database: EMDB / ID: EMD-68992
TitleCryo-EM structure of Oryza sativa vacuolar phosphate efflux transporter 2 (OsVPE2) at pH5.
Map data
Sample
  • Complex: O. sativa vacuolar phosphate efflux transporter 2
    • Protein or peptide: Os08g0156600 protein
Keywordsvacuolar phosphate efflux transporter / Monomer / TRANSPORT PROTEIN
Function / homology:
Function and homology information
Biological speciesOryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLiu Z / Cao S / Zou J
Funding support China, 1 items
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, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68992.png

Downloads & links

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Map

FileDownload / File: emd_68992.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.029141022 - 2.141774
Average (Standard dev.)0.00055097445 (±0.01403549)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68992_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_68992_half_map_2.map
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Sample components

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Entire : O. sativa vacuolar phosphate efflux transporter 2

EntireName: O. sativa vacuolar phosphate efflux transporter 2
Components
  • Complex: O. sativa vacuolar phosphate efflux transporter 2
    • Protein or peptide: Os08g0156600 protein

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Supramolecule #1: O. sativa vacuolar phosphate efflux transporter 2

SupramoleculeName: O. sativa vacuolar phosphate efflux transporter 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)

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Macromolecule #1: Os08g0156600 protein

MacromoleculeName: Os08g0156600 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 53.710336 KDa
Recombinant expressionOrganism: Homo heidelbergensis (Heidelberg man)
SequenceString: MAHSHEMTSR KPPGIRLFGG ITVLRTYQTL VLVLTFVAYT CFHMTRKIPS IVKSVLDPQT KLGSSPWGRL HTKNTLNIGW LPFNTIDGS ALLGEIDVAF LAVYSVGMFF AGHLGDRMDL RIFLTIGMFG TAVFTALFGA GYWLNIHNFY YFLVIQMIAG L FQAIGWPS ...String:
MAHSHEMTSR KPPGIRLFGG ITVLRTYQTL VLVLTFVAYT CFHMTRKIPS IVKSVLDPQT KLGSSPWGRL HTKNTLNIGW LPFNTIDGS ALLGEIDVAF LAVYSVGMFF AGHLGDRMDL RIFLTIGMFG TAVFTALFGA GYWLNIHNFY YFLVIQMIAG L FQAIGWPS VVAIVGNWFG KSKRGLIMGI WNAHTSVGNI SGSLLAAFLL KFGWGWSFAI PSLIMVAVGL LVFVFLPVSP EV MEIDIDD GEISSVKDTT KEPLLEPGQE VKHNAVGFLE AWKIPGVAPF ALCLFFSKLV AYTFLYWLPF YISHTPIGGE YLS DALAGS LSTIFDVGGV LGGVLAGHIS DRLNARAVTA ASFMYCAIPA LFLYRTYGSM SIMWNICLMF ITGMFVNGPY ALIT TAVSA DLGTHSSLNG NSRALATVTA IIDGTGSVGA AIGPLLTGYI SSSSWSAVFT MLMAAALLAG LLLTQLVCSE LKGKA TSNA SKDVADAQGT YSDEV

UniProtKB: UNIPROTKB: A0A0P0XCF9

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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 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 88308
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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