9X5U | pdb_00009x5u

Arabidopsis thaliana URE transporter DUR3 - URE bound

• PDB DOI: https://doi.org/10.2210/pdb9X5U/pdb
• EM Map EMD-66597: EMDB EMDataResource

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-10-14 Released: 2025-11-05 
• Deposition Author(s): Wang, Y.L., Lin, H.J., Zhang, J.R., Fan, M.R.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and mechanism of plant urea transporter DUR3.

Wang, Y., Green, M.N., Lin, H., Sander, A.M., Mazurek, C., Lin, X., Li, T., Wang, R., Li, W., Davis, G.V., Zhao, X., Zhu, L., Feng, P., Frommer, W.B., Zhang, J., Wudick, M.M., Fan, M.

(2026) New Phytol 250: 15-20

• PubMed: 41261797 
• DOI: https://doi.org/10.1111/nph.70752
• Primary Citation Related Structures: 
  9VIM, 9X5U

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Organizational Affiliation: 
• CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
Key Laboratory of Plant Carbon Capture, Chinese Academy of Sciences, Shanghai, 200032, China.
University of Chinese Academy of Sciences, Beijing, 101408, China.
Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200433, China.
Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
Institute for Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 322.89 kDa 
• Atom Count: 20,232 
• Modeled Residue Count: 2,660 
• Deposited Residue Count: 2,984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urea-proton symporter DUR3	A, B, C, D	746	Arabidopsis thaliana	Mutation(s): 0  Gene Names: DUR3, At5g45380, MFC19.5
UniProt
Find proteins for F4KD71 (Arabidopsis thaliana) Explore F4KD71  Go to UniProtKB:  F4KD71

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URE (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Wang, Y.L., Lin, H.J., Zhang, J.R., Fan, M.R.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB0630101

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release
  
• Version 1.1: 2026-05-27
  Changes: Data collection, Database references