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- EMDB-35459: Cryo-EM structure of an amyloid fibril formed by ALS-causing SOD1... -

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Basic information

Entry
Database: EMDB / ID: EMD-35459
TitleCryo-EM structure of an amyloid fibril formed by ALS-causing SOD1 mutation G85R
Map dataCryo-EM map of G85R fibril.
Sample
  • Organelle or cellular component: ALS-causing SOD1 mutations G85R
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
KeywordsAmyloid fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / regulation of organ growth / relaxation of vascular associated smooth muscle / anterograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to superoxide / regulation of T cell differentiation in thymus / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / myeloid cell homeostasis / regulation of GTPase activity / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / cellular response to ATP / superoxide dismutase activity / negative regulation of reproductive process / negative regulation of developmental process / transmission of nerve impulse / cellular response to cadmium ion / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / axon cytoplasm / embryo implantation / glutathione metabolic process / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / placenta development / response to amphetamine / thymus development / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / response to nutrient levels / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / 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 space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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: 2.97 Å
AuthorsWang LQ / Ma YY / Zhang MY / Yuan HY / Li XN / Zhao K / Chen J / Li D / Wang ZZ / Le WD ...Wang LQ / Ma YY / Zhang MY / Yuan HY / Li XN / Zhao K / Chen J / Li D / Wang ZZ / Le WD / Liu C / Liang Y
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271326 China
National Natural Science Foundation of China (NSFC)32071212 China
National Natural Science Foundation of China (NSFC)31770833 China
National Natural Science Foundation of China (NSFC)32201040 China
CitationJournal: Sci Adv / Year: 2024
Title: Amyloid fibril structures and ferroptosis activation induced by ALS-causing SOD1 mutations.
Authors: Wang LQ / Ma YY / Zhang MY / Yuan HY / Li XN / Zhao K / Chen J / Li D / Wang ZZ / Le WD / Liu C / Liang Y
History
DepositionFeb 23, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_35459.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of G85R fibril.
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.0117
Minimum - Maximum-0.03465871 - 0.06978249
Average (Standard dev.)0.0001154509 (±0.0018157669)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ALS-causing SOD1 mutations G85R

EntireName: ALS-causing SOD1 mutations G85R
Components
  • Organelle or cellular component: ALS-causing SOD1 mutations G85R
    • Protein or peptide: Superoxide dismutase [Cu-Zn]

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Supramolecule #1: ALS-causing SOD1 mutations G85R

SupramoleculeName: ALS-causing SOD1 mutations G85R / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 16.058899 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MATKAVCVLK GDGPVQGIIN FEQKESNGPV KVWGSIKGLT EGLHGFHVHE FGDNTAGCTS AGPHFNPLSR KHGGPKDEER HVGDLRNVT ADKDGVADVS IEDSVISLSG DHCIIGRTLV VHEKADDLGK GGNEESTKTG NAGSRLACGV IGIAQ

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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.87 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.058 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53707
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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