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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9X5U

This is version 1.0 of the entry. See complete history.

Literature

Arabidopsis thaliana URE transporter DUR3 - URE bound

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

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F4KD71
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URE (Subject of Investigation/LOI) Query on URE Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB0630101

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.