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- EMDB-81807: In situ structure of mouse urate oxidase assembly with helical sy... -

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Basic information

Entry
Database: EMDB / ID: EMD-81807
TitleIn situ structure of mouse urate oxidase assembly with helical symmetry applied
Map data
Sample
  • Organelle or cellular component: mouse hepatic peroxisomes
    • Protein or peptide: Uricase
  • Ligand: URIC ACID
Keywordsenzyme / OXIDOREDUCTASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsYang JH / Chen Z / Guo Q
Funding support China, 1 items
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 JH
History
DepositionJun 27, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_81807.png

Downloads & links

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Map

FileDownload / File: emd_81807.map.gz / Format: CCP4 / Size: 361.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 456 pix.
= 424.08 Å		0.93 Å/pix.
x 456 pix.
= 424.08 Å		0.93 Å/pix.
x 456 pix.
= 424.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.05172214 - 0.10240559
Average (Standard dev.)0.0005564128 (±0.0056804577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions456456456
Spacing456456456
CellA=B=C: 424.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_81807_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_81807_half_map_2.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 : mouse hepatic peroxisomes

EntireName: mouse hepatic peroxisomes
Components
  • Organelle or cellular component: mouse hepatic peroxisomes
    • Protein or peptide: Uricase
  • Ligand: URIC ACID

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Supramolecule #1: mouse hepatic peroxisomes

SupramoleculeName: mouse hepatic peroxisomes / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Uricase

MacromoleculeName: Uricase / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: factor-independent urate hydroxylase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 33.191148 KDa
SequenceString: EVEFVRTGYG KDMVKVLHIQ RDGKYHSIKE VATSVQLTLR SKKDYLHGDN SDIIPTDTIK NTVHVLAKLR GIRNIETFAM NICEHFLSS FNHVTRAHVY VEEVPWKRFE KNGIKHVHAF IHTPTGTHFC EVEQMRNGPP VIHSGIKDLK VLKTTQSGFE G FLKDQFTT ...String:
EVEFVRTGYG KDMVKVLHIQ RDGKYHSIKE VATSVQLTLR SKKDYLHGDN SDIIPTDTIK NTVHVLAKLR GIRNIETFAM NICEHFLSS FNHVTRAHVY VEEVPWKRFE KNGIKHVHAF IHTPTGTHFC EVEQMRNGPP VIHSGIKDLK VLKTTQSGFE G FLKDQFTT LPEVKDRCFA TQVYCKWRYQ RRDVDFEAIW GAVRDIVLQK FAGPYDKGEY SPSVQKTLYD IQVLSLSQLP EI EDMEISL PNIHYFNIDM SKMGLINKEE VLLPLDNPYG KITGTVKRKL

UniProtKB: Uricase

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Macromolecule #2: URIC ACID

MacromoleculeName: URIC ACID / type: ligand / ID: 2 / Number of copies: 24 / Formula: URC
Molecular weightTheoretical: 168.11 Da
Chemical component information

ChemComp-URC:
URIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

68843

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 219322
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

4mb8


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-43dy:
In situ structure of mouse urate oxidase assembly with helical symmetry applied

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