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

Arabidopsis thaliana URE transporter DUR3 - URE bound

Wang, Y.L., Lin, H.J., Zhang, J.R., Fan, M.R.

To be published.

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