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- PDB-31ez: UapA (Q408E) in MSP1E3D1 nanodiscs, Xanthine-bound state -

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Basic information

Entry
Database: PDB / ID: 31ez
TitleUapA (Q408E) in MSP1E3D1 nanodiscs, Xanthine-bound 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
ERGOSTEROL / MYRISTIC ACID / XANTHINE / Uric acid-xanthine permease
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 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: 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, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)123,19850
Polymers110,7062
Non-polymers12,49248
Water00
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

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


Mass: 55353.102 Da / Num. of mol.: 2 / Mutation: Q408E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: uapA, AN6932 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): FGY217 / References: UniProt: Q07307
#2: Chemical...
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical
ChemComp-ERG / ERGOSTEROL


Mass: 396.648 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C28H44O
#4: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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 (Q408E) in MSP1E3D1 nanodiscs, the in xanthine-bound 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: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54200 / Symmetry type: POINT
RefinementHighest resolution: 3.48 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028836
ELECTRON MICROSCOPYf_angle_d0.55311912
ELECTRON MICROSCOPYf_dihedral_angle_d6.7142204
ELECTRON MICROSCOPYf_chiral_restr0.0381370
ELECTRON MICROSCOPYf_plane_restr0.0041416

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