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- EMDB-68847: Subtomogram averaged rat UOX assembly map -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-68847
TitleSubtomogram averaged rat UOX assembly map
Map data
Sample
  • Tissue: rat UOX assembly isolated from liver tissue
    • Protein or peptide: urate oxidase
Keywordsenzyme / OXIDOREDUCTASE
Function / homology
Function and homology information


factor-independent urate hydroxylase / urate oxidase activity / purine nucleobase catabolic process / urate catabolic process / peroxisomal matrix / peroxisome
Similarity search - Function
Uricase, conserved site / Uricase signature. / Uricase / Uricase
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 10.0 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
DepositionJan 31, 2026-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68847.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.88 Å/pix.
x 128 pix.
= 496.64 Å		3.88 Å/pix.
x 128 pix.
= 496.64 Å		3.88 Å/pix.
x 128 pix.
= 496.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.264
Minimum - Maximum-0.6053 - 0.610076
Average (Standard dev.)0.0008134674 (±0.11934291)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 496.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68847_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_68847_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 : rat UOX assembly isolated from liver tissue

EntireName: rat UOX assembly isolated from liver tissue
Components
  • Tissue: rat UOX assembly isolated from liver tissue
    • Protein or peptide: urate oxidase

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Supramolecule #1: rat UOX assembly isolated from liver tissue

SupramoleculeName: rat UOX assembly isolated from liver tissue / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: urate oxidase

MacromoleculeName: urate oxidase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
SequenceString: MAHYHDDYGK NDEVEFVRTG YGKDMVKVLH IQRDGKYHSI KEVATSVQLT LRSKKDYLHG DNSDIIPTD TIKNTVHVLA KFKGIKSIET FAMNICEHFL SSFSHVTRAH VYVEEVPWKR F EKNGVKHV HAFIHTPTGT HFCDVEQVRN GPPIIHSGIK DLKVLKTTQS ...String:
MAHYHDDYGK NDEVEFVRTG YGKDMVKVLH IQRDGKYHSI KEVATSVQLT LRSKKDYLHG DNSDIIPTD TIKNTVHVLA KFKGIKSIET FAMNICEHFL SSFSHVTRAH VYVEEVPWKR F EKNGVKHV HAFIHTPTGT HFCDVEQVRN GPPIIHSGIK DLKVLKTTQS GFEGFIKDQF TT LPEVKDR CFATQVYCKW RYQNRDVDFE ATWGAVRDIV LKKFAGPYDR GEYSPSVQKT LYD IQVLTL SQLPEIEDME ISLPNIHYFN IDMSKMGLIN KEEVLLPLDN PYGKITGTVR RKLP SRL

UniProtKB: Uricase

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.36 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 13156
ExtractionNumber tomograms: 10 / Number images used: 17079 / Software: (Name: IMOD, Warp)
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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