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- PDB-31ey: UapA (Q408E) in DDM, Apo state -

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Basic information

Entry
Database: PDB / ID: 31ey
TitleUapA (Q408E) in DDM, Apo state
ComponentsUric acid-xanthine permease
KeywordsMEMBRANE PROTEIN / UapA / DDM / Transporter / Inward-facing / Uric Acid / Xanthine
Function / homology
Function and homology information


xanthine transport / xanthine transmembrane transporter activity / autophagosome lumen / purine nucleobase binding / urate transport / urate transmembrane transporter activity / fungal-type vacuole / endosome membrane / plasma membrane
Similarity search - Function
Xanthine/uracil permease / Xanthine/uracil permeases family signature. / Nucleobase cation symporter 2 family / Permease family
Similarity search - Domain/homology
LAURIC ACID / ERGOSTEROL / (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate / MYRISTIC ACID / PALMITIC ACID / Uric acid-xanthine permease
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsBroutzakis, G. / Gatsogiannis, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)496113311 Germany
German Research Foundation (DFG)211/667-1 Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Cryo-EM of the eukaryotic purine transporter UapA demonstrates intramolecular and lipid regulation of transport.
Authors: George Broutzakis / Yiannis Pyrris / Ifigeneia Akrani / Alexander Neuhaus / Emmanuel Mikros / George Diallinas / Christos Gatsogiannis /
Abstract: Members of the nucleobase ascorbate transporter (NAT) family (SLC23) are elevator-type transporters that are responsible for the uptake of nucleobases and ascorbate. In fungi, NAT members are also ...Members of the nucleobase ascorbate transporter (NAT) family (SLC23) are elevator-type transporters that are responsible for the uptake of nucleobases and ascorbate. In fungi, NAT members are also responsible for the specific uptake of antifungal nucleobase analogues, such as oxypurinol, allopurinol, or 8-azaguanine. Here, we report nearly full-length cryo-EM structures of UapA, a high-affinity purine transporter from the model fungus , in inward-facing apo- and substrate-loaded conformations at 2.06 to 3.5 Å in detergent and lipid nanodiscs. The high-resolution structures reveal the role of water molecules and lipids in substrate binding, specificity, transporter dimerization, and activity. Notably, the N-tail of UapA is found to be structured, interacting with both the core and scaffold domains, which in combination with functional data suggests a dual role in trafficking and transport dynamics. Overall, our study provides unprecedented structural and functional insights into an elevator-type fungal transporter, which may well contribute to the exploitation of NAT transporters as specific gateways for targeted pharmacological antifungal approaches.
History
DepositionJun 1, 2026Deposition site: PDBE / Processing site: PDBE
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uric acid-xanthine permease
B: Uric acid-xanthine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,84868
Polymers110,5082
Non-polymers21,34066
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein / Sugars , 2 types, 16 molecules AB

#1: Protein Uric acid-xanthine permease / UAPA transporter


Mass: 55253.984 Da / Num. of mol.: 2 / Mutation: Q408E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Strain: A4 / Gene: uapA, AN6932 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): FGY217 / References: UniProt: Q07307
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 6 types, 148 molecules

#3: Chemical...
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical
ChemComp-ERG / ERGOSTEROL


Mass: 396.648 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C28H44O
#6: Chemical
ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H24O2
#7: Chemical
ChemComp-FAW / (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate


Mass: 512.805 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H60O5
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: UapA (WT) in DDM, Apo state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: Aspergillus nidulans FGSC A4 (mold) / Strain: A4
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: FGY217
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2150 mMSodium ChlorideNaCl1
30.03 %DDMC24H46O111
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 286.15 K
Details: Vitrification chamber was allowed to equilibrate for 15 min at 100% humidity.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.1particle selection
2PHENIXmodel refinement
13cryoSPARC4.5.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180198 / Symmetry type: POINT
RefinementHighest resolution: 2.59 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039422
ELECTRON MICROSCOPYf_angle_d0.54712616
ELECTRON MICROSCOPYf_dihedral_angle_d10.9023094
ELECTRON MICROSCOPYf_chiral_restr0.041500
ELECTRON MICROSCOPYf_plane_restr0.0051420

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