23IF | pdb_000023if

Cryo-EM structure of Oryza sativa vacuolar phosphate efflux transporter 2 (OsVPE2) with phosphate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 23IF

This is version 1.1 of the entry. See complete history

Literature

Decoding plant vacuolar phosphate efflux: Structural and dynamic insights from rice VPE2.

Zuo, J.Cao, S.Tang, Y.He, H.Zhang, J.Li, P.Chen, Y.Yin, P.Wang, C.Xiong, L.Dong, F.Liu, Z.

(2026) Proc Natl Acad Sci U S A 123: e2611598123-e2611598123

  • DOI: https://doi.org/10.1073/pnas.2611598123
  • Primary Citation Related Structures: 
    23IC, 23IF, 23IG

  • PubMed 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 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.


  • Organizational Affiliation
    • National Key Laboratory of Crop Genetic Improvement, Hubei Provincial Research Center for Basic Biological Sciences, College of Bio-X, Hubei Hongshan Laboratory, Department of Biochemistry and Molecular Biology, Huazhong Agricultural University, Wuhan 430070, China.

Macromolecule Content 

  • Total Structure Weight: 53.81 kDa 
  • Atom Count: 3,246 
  • Modeled Residue Count: 427 
  • Deposited Residue Count: 499 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Os08g0156600 protein499Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: Os08g0156600
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
(Subject of Investigation/LOI)

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32422041

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release
  • Version 1.1: 2026-08-26
    Changes: Data collection, Database references