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- EMDB-67613: Cryo-EM structure of monomeric Cu/Zn-superoxide dismutase from do... -

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Basic information

Entry
Database: EMDB / ID: EMD-67613
TitleCryo-EM structure of monomeric Cu/Zn-superoxide dismutase from dog (Canis familiaris) complexed with 19A9 triabody in the open conformation
Map data
Sample
  • Complex: trivalent antibody fragment (triabody) - Cu/Zn-superoxide dismutase complex
    • Protein or peptide: trivalent antibody fragment (triabody)
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
KeywordsCu/Zn-superoxide dismutase (SOD1) / neurodegenerative disease / antibody / METAL BINDING PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / reactive oxygen species metabolic process / peroxisome / copper ion binding / mitochondrion / nucleus / cytosol
Similarity search - Function
Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesCanis lupus familiaris (dog) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsShino Y / Furukawa Y / Muraki N
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05765 Japan
Japan Society for the Promotion of Science (JSPS)22H02768 Japan
Japan Society for the Promotion of Science (JSPS)22K19389 Japan
CitationJournal: Protein Sci / Year: 2026
Title: Structural analysis of Cu/Zn-superoxide dismutase linked to neurodegenerative disease by antibody-guided cryo-EM.
Authors: Yuki Shino / Norifumi Muraki / Yui Kobatake / Hiroaki Kamishina / Hirofumi Kosuge / Makoto Nakakido / Kouhei Tsumoto / Yoshiaki Furukawa /
Abstract: Accumulation of misfolded proteins is a hallmark of many neurodegenerative diseases. To characterize such misfolded species in vivo, conformation-specific antibodies are widely used; however, limited ...Accumulation of misfolded proteins is a hallmark of many neurodegenerative diseases. To characterize such misfolded species in vivo, conformation-specific antibodies are widely used; however, limited knowledge of antibody-epitope interactions often hampers mechanistic insight. To address this, we determined the cryo-electron microscopy structure of the complex between a monoclonal antibody, 19A9, and Cu/Zn-superoxide dismutase (SOD1), a protein associated with canine degenerative myelopathy (DM), which is related to human amyotrophic lateral sclerosis. Biochemical analyses confirmed that 19A9 specifically recognizes monomeric SOD1, and the structure revealed binding near the interface normally used for homodimerization in native SOD1, with steric hindrance preventing interaction when the protein is in its homodimeric form. Immunofluorescence staining of spinal cord sections revealed that 19A9 stained a subset of motoneurons in DM-affected dogs, but not in asymptomatic controls. Structural characterization of the 19A9-monomeric SOD1 complex enabled us to propose that SOD1 monomers can arise in vivo under pathological conditions.
History
DepositionDec 10, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67613.png

Downloads & links

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Map

FileDownload / File: emd_67613.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 300.8 Å		0.75 Å/pix.
x 400 pix.
= 300.8 Å		0.75 Å/pix.
x 400 pix.
= 300.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-1.3203918 - 2.0662675
Average (Standard dev.)0.00069632207 (±0.029751517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 300.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67613_msk_1.map
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Half map: #1

Fileemd_67613_half_map_1.map
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Half map: #2

Fileemd_67613_half_map_2.map
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Sample components

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Entire : trivalent antibody fragment (triabody) - Cu/Zn-superoxide dismuta...

EntireName: trivalent antibody fragment (triabody) - Cu/Zn-superoxide dismutase complex
Components
  • Complex: trivalent antibody fragment (triabody) - Cu/Zn-superoxide dismutase complex
    • Protein or peptide: trivalent antibody fragment (triabody)
    • Protein or peptide: Superoxide dismutase [Cu-Zn]

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Supramolecule #1: trivalent antibody fragment (triabody) - Cu/Zn-superoxide dismuta...

SupramoleculeName: trivalent antibody fragment (triabody) - Cu/Zn-superoxide dismutase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Canis lupus familiaris (dog)

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Macromolecule #1: trivalent antibody fragment (triabody)

MacromoleculeName: trivalent antibody fragment (triabody) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.39343 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQIQLVQSGP DLKKPGETVK ISCKASGYPF TNYGMNWVKQ APGKGLKWIG LINTYTGEPT YADDFKGRFA FSLETSASTA YLQINNLKN EDTATYFCAR PGTSPRYGYN GYFDVWGAGT TVTVSSDIVM TQSQKFMSTS VGDRVSITCK ASQNVGTAVA W YQQKPGQS ...String:
MQIQLVQSGP DLKKPGETVK ISCKASGYPF TNYGMNWVKQ APGKGLKWIG LINTYTGEPT YADDFKGRFA FSLETSASTA YLQINNLKN EDTATYFCAR PGTSPRYGYN GYFDVWGAGT TVTVSSDIVM TQSQKFMSTS VGDRVSITCK ASQNVGTAVA W YQQKPGQS PKLLIYSASN RCTGVPDRFI GSGSGTDFTL TISNMQSEDL ANYFCQQYSS YPFTFGGGTK LEIK

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Macromolecule #2: Superoxide dismutase [Cu-Zn]

MacromoleculeName: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 15.918711 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEMKAVCVLK GQGPVEGTIH FVQKGSGPVV VSGTITGLTE GEHGFHVHQE EDNTQGCTSA GPHFNPLSKK HGGPKDQERH VGDLGNVTA GKDGVAIVSI EDSLIALSGD YSIIGRTMVV HEKRDDLGKG DNEESTQTGN AGSRLACGVI GIAQ

UniProtKB: Superoxide dismutase [Cu-Zn]

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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

Concentration10 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.66 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60575
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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