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- PDB-9j7d: Arabidopsis high-affinity urea transport DUR3 in the inward-facin... -

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Basic information

Entry
Database: PDB / ID: 9j7d
TitleArabidopsis high-affinity urea transport DUR3 in the inward-facing open conformation, dimeric state
ComponentsUrea-proton symporter DUR3
KeywordsMEMBRANE PROTEIN / DUR3 / high-affinity urea transporter / urea transporter
Function / homology
Function and homology information


urea transmembrane transporter activity / urea transmembrane transport / symporter activity / cellular response to nitrogen starvation / plasma membrane
Similarity search - Function
Urea active transporter / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile.
Similarity search - Domain/homology
TETRADECANE / HEXADECANE / CHOLESTEROL HEMISUCCINATE / Urea-proton symporter DUR3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsAn, W. / Gao, Y. / Zhang, X.C.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030304 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of urea transport by Arabidopsis thaliana DUR3.
Authors: Weidong An / Yiwei Gao / Laihua Liu / Qinru Bai / Jun Zhao / Yan Zhao / Xuejun C Zhang /
Abstract: Urea is a primary nitrogen source used as fertilizer in agricultural plant production and a crucial nitrogen metabolite in plants, playing an essential role in modern agriculture. In plants, DUR3 is ...Urea is a primary nitrogen source used as fertilizer in agricultural plant production and a crucial nitrogen metabolite in plants, playing an essential role in modern agriculture. In plants, DUR3 is a proton-driven high-affinity urea transporter located on the plasma membrane. It not only absorbs external low-concentration urea as a nutrient but also facilitates nitrogen transfer by recovering urea from senescent leaves. Despite its importance, the high-affinity urea transport mechanism in plants remains insufficiently understood. In this study, we determine the structures of Arabidopsis thaliana DUR3 in two different conformations: the inward-facing open state of the apo structure and the occluded urea-bound state, with overall resolutions of 2.8 Å and 3.0 Å, respectively. By comparing these structures and analyzing their functional characteristics, we elucidated how urea molecules are specifically recognized. In the urea-bound structure, we identified key titratable amino acid residues and proposed a model for proton involvement in urea transport based on structural and functional data. This study enhances our understanding of proton-driven urea transport mechanisms in DUR3.
History
DepositionAug 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urea-proton symporter DUR3
B: Urea-proton symporter DUR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5539
Polymers151,9552
Non-polymers2,5987
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Urea-proton symporter DUR3 / AtDUR3 / High-affinity urea active transporter DUR3


Mass: 75977.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DUR3, At5g45380, MFC19.5 / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: F4KD71
#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C31H50O4
#3: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H30
#4: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C16H34
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Arabidopsis high-affinity urea transporter / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
12cryoSPARCclassification
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73561 / Symmetry type: POINT

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