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- PDB-23bt: Structure of mouse urate oxidase in complex with uric acid -

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Basic information

Entry
Database: PDB / ID: 23bt
TitleStructure of mouse urate oxidase in complex with uric acid
ComponentsUricase
KeywordsOXIDOREDUCTASE / enzyme
Function / homology
Function and homology information


hypoxanthine catabolic process / guanine catabolic process / deoxyguanosine catabolic process / xanthine catabolic process / GMP catabolic process / deoxyinosine catabolic process / deoxyadenosine catabolic process / inosine catabolic process / dAMP catabolic process / AMP catabolic process ...hypoxanthine catabolic process / guanine catabolic process / deoxyguanosine catabolic process / xanthine catabolic process / GMP catabolic process / deoxyinosine catabolic process / deoxyadenosine catabolic process / inosine catabolic process / dAMP catabolic process / AMP catabolic process / dGMP catabolic process / adenosine catabolic process / IMP catabolic process / factor-independent urate hydroxylase / urate oxidase activity / purine nucleobase catabolic process / urate catabolic process / purine nucleobase metabolic process / peroxisome / mitochondrion / cytosol
Similarity search - Function
Uricase, conserved site / Uricase signature. / Uricase / Uricase
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsYang, J.H. / Chen, Z. / Guo, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A conserved supramolecular architecture of urate oxidase organizes metabolism in peroxisomes
Authors: Yang, J.H.
History
DepositionJan 31, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 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: Uricase
B: Uricase
C: Uricase
D: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,4688
Polymers131,7964
Non-polymers6724
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
Uricase / Urate oxidase


Mass: 32948.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Uox / Production host: Escherichia coli (E. coli)
References: UniProt: P25688, factor-independent urate hydroxylase
#2: Chemical
ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N4O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: urate oxidase with uric acid / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304325 / Symmetry type: POINT
RefinementHighest resolution: 2.42 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049548
ELECTRON MICROSCOPYf_angle_d0.56512908
ELECTRON MICROSCOPYf_dihedral_angle_d4.8331236
ELECTRON MICROSCOPYf_chiral_restr0.0471416
ELECTRON MICROSCOPYf_plane_restr0.0051636

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