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- EMDB-63109: Cryo-EM structure of human SOD1 (G93A) amyloid filament -

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Basic information

Entry
Database: EMDB / ID: EMD-63109
TitleCryo-EM structure of human SOD1 (G93A) amyloid filament
Map data
Sample
  • Complex: An amyloid filament of human G93A mutant SOD1 protein
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
Keywordsamyloid / filament / superoxide dismutase 1 / amyotrophic lateral sclerosis / PROTEIN FIBRIL
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / relaxation of vascular associated smooth muscle / dense core granule / regulation of organ growth / response to superoxide / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / relaxation of vascular associated smooth muscle / dense core granule / regulation of organ growth / response to superoxide / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / protein phosphatase 2B binding / regulation of T cell differentiation in thymus / anterograde axonal transport / Oxidoreductases; Acting on a sulfur group of donors / regulation of GTPase activity / retina homeostasis / auditory receptor cell stereocilium organization / cellular response to potassium ion / hydrogen peroxide biosynthetic process / retrograde axonal transport / myeloid cell homeostasis / superoxide anion generation / superoxide metabolic process / response to copper ion / superoxide dismutase / muscle cell cellular homeostasis / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / heart contraction / cellular response to cadmium ion / cellular response to ATP / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / ovarian follicle development / neuronal action potential / positive regulation of superoxide anion generation / axon cytoplasm / removal of superoxide radicals / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of phagocytosis / dendrite cytoplasm / placenta development / thymus development / positive regulation of cytokine production / determination of adult lifespan / regulation of mitochondrial membrane potential / response to amphetamine / glutathione metabolic process / response to hydrogen peroxide / locomotory behavior / sensory perception of sound / response to nutrient levels / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / Platelet degranulation / peroxisome / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / gene expression / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / response to ethanol / positive regulation of MAPK cascade / lysosome / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / : / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Copper/Zinc superoxide dismutase signature 1. / 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 speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.74 Å
AuthorsBaek Y / Ha N-C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Amyloid filament structure of human G93A mutant SOD1
Authors: Baek Y / Kim H / Lee H / Lee H / Roh S-H / Ha N-C
History
DepositionJan 13, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63109.png

Downloads & links

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Map

FileDownload / File: emd_63109.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 330 pix.
= 250.8 Å		0.76 Å/pix.
x 330 pix.
= 250.8 Å		0.76 Å/pix.
x 330 pix.
= 250.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.015315643 - 0.020039724
Average (Standard dev.)0.00007667547 (±0.0007734617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 250.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63109_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_63109_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 : An amyloid filament of human G93A mutant SOD1 protein

EntireName: An amyloid filament of human G93A mutant SOD1 protein
Components
  • Complex: An amyloid filament of human G93A mutant SOD1 protein
    • Protein or peptide: Superoxide dismutase [Cu-Zn]

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Supramolecule #1: An amyloid filament of human G93A mutant SOD1 protein

SupramoleculeName: An amyloid filament of human G93A mutant SOD1 protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.6 kDa/nm

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Macromolecule #1: Superoxide dismutase [Cu-Zn]

MacromoleculeName: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.720596 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAMDPEFMAT KAVCVLKGDG PVQGIINFEQ KESNGPVKVW GSIKGLTEGL HGFHVHEFGD NTAGCTSAGP HFNPLSRKHG GPKDEERHV GDLGNVTADK DAVADVSIED SVISLSGDHC IIGRTLVVHE KADDLGKGGN EESTKTGNAG SRLACGVIGI A Q

UniProtKB: Superoxide dismutase [Cu-Zn]

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 3962 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.84 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.87 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 50301
CTF correctionSoftware - Name: RELION (ver. 5.0) / Software - details: CTFFIND-4.1 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 56754 / Software - Name: RELION (ver. 5.0) / Software - details: start-end manual picking
Startup modelType of model: NONE / Details: used relion_helix_inimodel2d program
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9jbo


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial global fitting was done using USCF ChimeraX. Local fitting was done using Coot. PHENIX was used for flexible fitting.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9li1:
Cryo-EM structure of human SOD1 (G93A) amyloid filament

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