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- EMDB-61202: Arabidopsis high-affinity urea transport DUR3 in the inward-facin... -

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Basic information

Entry
Database: EMDB / ID: EMD-61202
TitleArabidopsis high-affinity urea transport DUR3 in the inward-facing open conformation, dimeric state
Map data
Sample
  • Complex: Arabidopsis high-affinity urea transporter
    • Protein or peptide: Urea-proton symporter DUR3
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: TETRADECANE
  • Ligand: HEXADECANE
  • Ligand: water
KeywordsDUR3 / high-affinity urea transporter / urea transporter / MEMBRANE PROTEIN
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-proton symporter DUR3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsAn W / Gao Y / Zhang XC
Funding support China, 1 items
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, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61202.png

Downloads & links

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Map

FileDownload / File: emd_61202.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.66139996 - 0.98289573
Average (Standard dev.)-0.0004149251 (±0.016623579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61202_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_61202_half_map_2.map
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Sample components

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Entire : Arabidopsis high-affinity urea transporter

EntireName: Arabidopsis high-affinity urea transporter
Components
  • Complex: Arabidopsis high-affinity urea transporter
    • Protein or peptide: Urea-proton symporter DUR3
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: TETRADECANE
  • Ligand: HEXADECANE
  • Ligand: water

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Supramolecule #1: Arabidopsis high-affinity urea transporter

SupramoleculeName: Arabidopsis high-affinity urea transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Urea-proton symporter DUR3

MacromoleculeName: Urea-proton symporter DUR3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 75.977445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATCPPFDFS TKYYDGDGGC QRQSSFFGGT TVLDQGVGYA VILGFGAFFA VFTSFLVWLE KRYVGARHTS EWFNTAGRNV KTGLIASVI VSQWTWAATI LQSSNVAWQY GVSGPFWYAS GATIQVLLFG VMAIEIKRKA PNAHTVCEIV KARWGTATHI V FLVFCLAT ...String:
MATCPPFDFS TKYYDGDGGC QRQSSFFGGT TVLDQGVGYA VILGFGAFFA VFTSFLVWLE KRYVGARHTS EWFNTAGRNV KTGLIASVI VSQWTWAATI LQSSNVAWQY GVSGPFWYAS GATIQVLLFG VMAIEIKRKA PNAHTVCEIV KARWGTATHI V FLVFCLAT NVVVTAMLLL GGSAVVNALT GVNLYAASFL IPLGVVVYTL AGGLKATFLA SYVHSVIVHV ALVVFVFLVY TS SKELGSP SVVYDRLKDM VAKSRSCTEP LSHHGQACGP VDGNFRGSYL TMLSSGGAVF GLINIVGNFG TVFVDNGYWV SAI AARPSS THKGYLLGGL VWFAVPFSLA TSLGLGALAL DLPISKDEAD RGLVPPATAI ALMGKSGSLL LLTMLFMAVT SAGS SELIA VSSLFTYDIY RTYINPRATG RQILKISRCA VLGFGCFMGI LAVVLNKAGV SLGWMYLAMG VLIGSAVIPI AFMLL WSKA NAFGAILGAT SGCVFGIITW LTTAKTQYGR VDLDSTGKNG PMLAGNLVAI LTGGLIHAVC SLVRPQNYDW STTREI KVV EAYASGDEDV DVPAEELREE KLRRAKAWIV KWGLVFTILI VVIWPVLSLP ARVFSRGYFW FWAIVAIAWG TIGSIVI IG LPLVESWDTI KSVCMGMFTN DRVMKKLDDL NHRLRALTMA VPEAEKIYLL ELEKTKKNDE EG

UniProtKB: Urea-proton symporter DUR3

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 3 / Number of copies: 1 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #4: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 4 / Number of copies: 2 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration15 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
In silico model: The insilico model was generated using the ab-initio reconstruction in cryoSPARC.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73561
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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