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- PDB-43dy: In situ structure of mouse urate oxidase assembly with helical sy... -

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Basic information

Entry
Database: PDB / ID: 43dy
TitleIn situ structure of mouse urate oxidase assembly with helical symmetry applied
ComponentsUricase
KeywordsOXIDOREDUCTASE / enzyme
Function / homology
Function and homology information


hypoxanthine catabolic process / guanine catabolic process / deoxyguanosine catabolic process / xanthine catabolic process / deoxyinosine catabolic process / deoxyadenosine catabolic process / GMP catabolic process / inosine catabolic process / dAMP catabolic process / AMP catabolic process ...hypoxanthine catabolic process / guanine catabolic process / deoxyguanosine catabolic process / xanthine catabolic process / deoxyinosine catabolic process / deoxyadenosine catabolic process / GMP catabolic process / inosine catabolic process / dAMP catabolic process / AMP catabolic process / IMP catabolic process / adenosine catabolic process / dGMP 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: 3.72 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
DepositionJun 27, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 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
E: Uricase
F: Uricase
G: Uricase
H: Uricase
I: Uricase
J: Uricase
K: Uricase
L: Uricase
M: Uricase
N: Uricase
O: Uricase
P: Uricase
Q: Uricase
R: Uricase
S: Uricase
T: Uricase
U: Uricase
V: Uricase
W: Uricase
X: Uricase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)800,62248
Polymers796,58824
Non-polymers4,03524
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: 33191.148 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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.: 24 / 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: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mouse hepatic peroxisomes / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 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
1RELION5.1particle selection
12cryoSPARC4.6.03D reconstruction
13PHENIX1.16-3549model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219322 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 10 / Num. of volumes extracted: 18138
Atomic model buildingPDB-ID: 4mb8

4mb8


Accession code: 4mb8 / Source name: PDB / Type: experimental model

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