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- EMDB-66597: Arabidopsis thaliana URE transporter DUR3 - URE bound -

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Basic information

Entry
Database: EMDB / ID: EMD-66597
TitleArabidopsis thaliana URE transporter DUR3 - URE bound
Map data
Sample
  • Complex: Arabidopsis thaliana URE transporter DUR3 - URE bound
    • Protein or peptide: Urea-proton symporter DUR3
  • Ligand: UREA
KeywordsURE transporter / homotetramer / PLANT 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: 3.19 Å
AuthorsWang YL / Lin HJ / Zhang JR / Fan MR
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0630101 China
CitationJournal: To Be Published
Title: Arabidopsis thaliana URE transporter DUR3 - URE bound
Authors: Wang YL / Lin HJ / Zhang JR / Fan MR
History
DepositionOct 14, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66597.png

Downloads & links

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Map

FileDownload / File: emd_66597.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 360 pix.
= 345.6 Å		0.96 Å/pix.
x 360 pix.
= 345.6 Å		0.96 Å/pix.
x 360 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.28429615 - 0.64350367
Average (Standard dev.)0.0012058489 (±0.017986175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66597_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66597_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66597_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana URE transporter DUR3 - URE bound

EntireName: Arabidopsis thaliana URE transporter DUR3 - URE bound
Components
  • Complex: Arabidopsis thaliana URE transporter DUR3 - URE bound
    • Protein or peptide: Urea-proton symporter DUR3
  • Ligand: UREA

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Supramolecule #1: Arabidopsis thaliana URE transporter DUR3 - URE bound

SupramoleculeName: Arabidopsis thaliana URE transporter DUR3 - URE bound / 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: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 80.662406 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 EGVDELTSRG RDYKDDDD K WSHPQFEKGG GGSGGSAWSH PQFEK

UniProtKB: Urea-proton symporter DUR3

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Macromolecule #2: UREA

MacromoleculeName: UREA / type: ligand / ID: 2 / Number of copies: 4 / Formula: URE
Molecular weightTheoretical: 60.055 Da
Chemical component information

ChemComp-URE:
UREA

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 174450
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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