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- EMDB-65093: Zea mays URE transporter DUR3 - URE bound -

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Basic information

Entry
Database: EMDB / ID: EMD-65093
TitleZea mays URE transporter DUR3 - URE bound
Map data
Sample
  • Complex: Zea mays URE transporter DUR3
    • Protein or peptide: Urea-proton symporter DUR3
  • Ligand: UREA
KeywordsURE transporter / homomeric tetramer / CHOLINE-BINDING PROTEIN
Function / homologyUrea active transporter / urea transmembrane transporter activity / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile. / urea transmembrane transport / plasma membrane / Urea-proton symporter DUR3
Function and homology information
Biological speciesZea mays (maize)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 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: Zea mays URE transporter DUR3 - URE bound
Authors: Wang YL / Lin HJ / Zhang JR / Fan MR
History
DepositionJun 18, 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_65093.png

Downloads & links

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Map

FileDownload / File: emd_65093.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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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

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.0018332133 - 1.8927932
Average (Standard dev.)0.00093216787 (±0.021391112)
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_65093_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65093_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65093_half_map_2.map
Projections & Slices
AxesZYX

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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 : Zea mays URE transporter DUR3

EntireName: Zea mays URE transporter DUR3
Components
  • Complex: Zea mays URE transporter DUR3
    • Protein or peptide: Urea-proton symporter DUR3
  • Ligand: UREA

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Supramolecule #1: Zea mays URE transporter DUR3

SupramoleculeName: Zea mays URE transporter DUR3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Zea mays (maize)

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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: Zea mays (maize)
Molecular weightTheoretical: 82.153883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAGGAGACP PPGLGFGGEY YSVVDGACSR DGSFFGGKPV LAQAVGYAVV LGFGAFFALF TSFLVWLEKR YVGSQHTSEW FNTAGRSVK TGLIASVIVS QWTWAATILQ SSNVAWQYGV SGPFWYASGA TIQVLLFGVM AIEIKRKAPK AHTVCEIVRA R WGRAAHAV ...String:
MAAGGAGACP PPGLGFGGEY YSVVDGACSR DGSFFGGKPV LAQAVGYAVV LGFGAFFALF TSFLVWLEKR YVGSQHTSEW FNTAGRSVK TGLIASVIVS QWTWAATILQ SSNVAWQYGV SGPFWYASGA TIQVLLFGVM AIEIKRKAPK AHTVCEIVRA R WGRAAHAV FLAFCLATNV IVTAMLLLGG SAVVNALTAI NVYAASFLIP LGVVVYTLAG GLKATFLASY IHSVVVHVVL VV FVFLVYT SGNRLGSPRV VHDHLTAVAS AVRNCSAPLS HPDQACGPVH GNFKGSYLTM LSSGGLVFGI INIVGNFGTV FVD NGYWMS AIAARPSSTH KGYLLGGLVW FAVPFSLATS LGLGALALDL PITAAEAAKG LVPAATATAL MGKSGSVLLL IMLF MAVTS AGSAELVAVS SLCTYDIYRT YINPDATGEQ ILRVSRATVL VFGCLMGVLA VILNLVGVSL GWLYLAMGVI IGSAV IPIA LLLLWRKANA LGAILGAVSG CVLGVTVWLS VAKVQYGRVD LDSTGRNAPM LAGNLVSILV GGAVHAACSL AWPQHY DWE SSRQITTVES VPADSDLAEE LKEERLVHAK RWIIKWGVAF TAVIAVVWPV LSLPAGRYSA GYFTMWAVIA IAWGTVG SA VIIFLPLVES WDTICKVCEG MFTNNAVYER LDEMNLRLKA IMGDMPEAEE RYQEMQKEKD LGTMEMVHPA SGTRPSIV A NDDEDNLSLA VDELTSRGRD YKDDDDKWSH PQFEKGGGGS GGSAWSHPQF EK

UniProtKB: Urea-proton symporter DUR3

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Macromolecule #2: UREA

MacromoleculeName: UREA / type: ligand / ID: 2 / Number of copies: 1 / 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: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
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: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 248055
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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