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Basic information

Entry
Database: EMDB / ID: EMD-58353
TitleUapA (Q408E) in DDM, Apo state
Map dataUnsharpened map
Sample
  • Complex: UapA (WT) in DDM, Apo state
    • Protein or peptide: Uric acid-xanthine permease
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: MYRISTIC ACID
  • Ligand: PALMITIC ACID
  • Ligand: ERGOSTEROL
  • Ligand: LAURIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate
  • Ligand: water
KeywordsUapA / DDM / Transporter / Inward-facing / Uric Acid / Xanthine / MEMBRANE PROTEIN
Biological speciesAspergillus nidulans FGSC A4 (mold)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsBroutzakis G / Gatsogiannis C
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)496113311 Germany
German Research Foundation (DFG)211/667-1 Germany
CitationJournal: To Be Published
Title: Cryo-EM of the eukaryotic purine transporter UapA demonstrates intramolecular and lipid regulation of transport
Authors: Broutzakis G / Pyrris Y / Akrani I / Neuhaus A / Mikros E / Diallinas G / Gatsogiannis C
History
DepositionJun 1, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58353.png

Downloads & links

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Map

FileReleased
AnnotationUnsharpened map
Voxel sizeX=Y=Z: 1.0063 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.2539735 - 0.55345964
Average (Standard dev.)0.0012450459 (±0.013806296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 257.6128 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58353_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : UapA (WT) in DDM, Apo state

EntireName: UapA (WT) in DDM, Apo state
Components
  • Complex: UapA (WT) in DDM, Apo state
    • Protein or peptide: Uric acid-xanthine permease
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: MYRISTIC ACID
  • Ligand: PALMITIC ACID
  • Ligand: ERGOSTEROL
  • Ligand: LAURIC ACID
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate
  • Ligand: water

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Supramolecule #1: UapA (WT) in DDM, Apo state

SupramoleculeName: UapA (WT) in DDM, Apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aspergillus nidulans FGSC A4 (mold) / Strain: A4
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Uric acid-xanthine permease

MacromoleculeName: Uric acid-xanthine permease / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aspergillus nidulans FGSC A4 (mold) / Strain: A4
Molecular weightTheoretical: 55.253984 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: VRLLARHLTT REGLIGDYDY GFLFRPELPF MKKDPRAPPF FGLNEKIPVL LAFILGLQHA LAMLAGVVTP PLIISSSLSL PSDLQQYLV STSLIVCGLL SMVQITRFHI YKTPYYIGSG VLSVMGVSFS IISVASGAFN QMYSNGFCQL DEAGNRLPCP E AYGALIGT ...String:
VRLLARHLTT REGLIGDYDY GFLFRPELPF MKKDPRAPPF FGLNEKIPVL LAFILGLQHA LAMLAGVVTP PLIISSSLSL PSDLQQYLV STSLIVCGLL SMVQITRFHI YKTPYYIGSG VLSVMGVSFS IISVASGAFN QMYSNGFCQL DEAGNRLPCP E AYGALIGT SACCALVEIL LAFVPPKVIQ KIFPPIVTGP TVMLIGISLI GTGFKDWAGG SACMDDGMLC PSATAPRPLP WG SPEFIGL GFLVFVSIIL CERFGAPIMK SCSVVIGLLV GCIVAAACGY FSHADIDAAP AASFIWVKTF PLSVYGPMVL PII AVFIIC ACECIGDVTA TCDVSRLEVR GGTFESRIQG AVLADGINSV VAALATMTPM TTFAENNGVI ALTRCANRWA GYCC CLILI VAGIFAKFAA AIVAIPNSVM GGMKTFLFAS VVISGQAIVA KAPFTRRNRF ILTASMALGY GATLVPTWFG NVFPQ TENR DLEGFENAIE LVLETGFAVT AFVAMLLNAI MPAEVS

UniProtKB: Uric acid-xanthine permease

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Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 14 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #3: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 3 / Number of copies: 22 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID

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Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 6 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #5: ERGOSTEROL

MacromoleculeName: ERGOSTEROL / type: ligand / ID: 5 / Number of copies: 8 / Formula: ERG
Molecular weightTheoretical: 396.648 Da
Chemical component information

ChemComp-ERG:
ERGOSTEROL

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Macromolecule #6: LAURIC ACID

MacromoleculeName: LAURIC ACID / type: ligand / ID: 6 / Number of copies: 12 / Formula: DAO
Molecular weightTheoretical: 200.318 Da
Chemical component information

ChemComp-DAO:
LAURIC ACID

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Macromolecule #7: (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate

MacromoleculeName: (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate / type: ligand / ID: 7 / Number of copies: 4 / Formula: FAW
Molecular weightTheoretical: 512.805 Da
Chemical component information

ChemComp-FAW:
(2S)-3-hydroxypropane-1,2-diyl ditetradecanoate

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 96 / 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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium Chloride
0.03 %C24H46O11DDM
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286.15 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification chamber was allowed to equilibrate for 15 min at 100% humidity..

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Electron microscopy

MicroscopeTFS KRIOS
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 180198
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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