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- EMDB-68840: Cryo-EM map of mouse urate oxidase in complex with uric acid -

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Basic information

Entry
Database: EMDB / ID: EMD-68840
TitleCryo-EM map of mouse urate oxidase in complex with uric acid
Map data
Sample
  • Complex: urate oxidase with uric acid
    • 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 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_68840.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 192 pix.
= 142.08 Å		0.74 Å/pix.
x 192 pix.
= 142.08 Å		0.74 Å/pix.
x 192 pix.
= 142.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.156
Minimum - Maximum-0.55285007 - 0.8843705
Average (Standard dev.)0.00009213158 (±0.051954966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 142.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68840_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68840_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 : urate oxidase with uric acid

EntireName: urate oxidase with uric acid
Components
  • Complex: urate oxidase with uric acid
    • Protein or peptide: Uricase
  • Ligand: URIC ACID

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Supramolecule #1: urate oxidase with uric acid

SupramoleculeName: urate oxidase with uric acid / type: complex / 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: 4 / Enantiomer: LEVO / EC number: factor-independent urate hydroxylase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 32.948879 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VEFVRTGYGK DMVKVLHIQR DGKYHSIKEV ATSVQLTLRS KKDYLHGDNS DIIPTDTIKN TVHVLAKLRG IRNIETFAMN ICEHFLSSF NHVTRAHVYV EEVPWKRFEK NGIKHVHAFI HTPTGTHFCE VEQMRNGPPV IHSGIKDLKV LKTTQSGFEG F LKDQFTTL ...String:
VEFVRTGYGK DMVKVLHIQR DGKYHSIKEV ATSVQLTLRS KKDYLHGDNS DIIPTDTIKN TVHVLAKLRG IRNIETFAMN ICEHFLSSF NHVTRAHVYV EEVPWKRFEK NGIKHVHAFI HTPTGTHFCE VEQMRNGPPV IHSGIKDLKV LKTTQSGFEG F LKDQFTTL PEVKDRCFAT QVYCKWRYQR RDVDFEAIWG AVRDIVLQKF AGPYDKGEYS PSVQKTLYDI QVLSLSQLPE IE DMEISLP NIHYFNIDMS KMGLINKEEV LLPLDNPYGK ITGTVKRK

UniProtKB: Uricase

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Macromolecule #2: URIC ACID

MacromoleculeName: URIC ACID / type: ligand / ID: 2 / Number of copies: 4 / 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 stateparticle

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Sample preparation

BufferpH: 8
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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4mb8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 304325
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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