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- PDB-9x5u: Arabidopsis thaliana URE transporter DUR3 - URE bound -

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Basic information

Entry
Database: PDB / ID: 9x5u
TitleArabidopsis thaliana URE transporter DUR3 - URE bound
ComponentsUrea-proton symporter DUR3
KeywordsPLANT PROTEIN / URE transporter / homotetramer
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
UREA / Urea-proton symporter DUR3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsWang, Y.L. / Lin, H.J. / Zhang, J.R. / Fan, M.R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0630101 China
CitationJournal: To Be Published
Title: Arabidopsis thaliana URE transporter DUR3 - URE bound
Authors: Wang, Y.L. / Lin, H.J. / Zhang, J.R. / Fan, M.R.
History
DepositionOct 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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
C: Urea-proton symporter DUR3
D: Urea-proton symporter DUR3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,8908
Polymers322,6504
Non-polymers2404
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 80662.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DUR3, At5g45380, MFC19.5 / Production host: Homo sapiens (human) / References: UniProt: F4KD71
#2: Chemical
ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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 thaliana URE transporter DUR3 - URE bound / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174450 / Symmetry type: POINT
RefinementHighest resolution: 3.19 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00320716
ELECTRON MICROSCOPYf_angle_d0.55628208
ELECTRON MICROSCOPYf_dihedral_angle_d4.2552832
ELECTRON MICROSCOPYf_chiral_restr0.0393348
ELECTRON MICROSCOPYf_plane_restr0.0043420

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