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- EMDB-32227: Cryo-EM structure of amyloid fibril formed by full-length human SOD1 -

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Basic information

Entry
Database: EMDB / ID: EMD-32227
TitleCryo-EM structure of amyloid fibril formed by full-length human SOD1
Map dataThe cryo-EM map of SOD1 fibril.
Sample
  • Organelle or cellular component: Human SOD1 amyloid fibril
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
KeywordsAmyloid fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / peripheral nervous system myelin maintenance / response to superoxide / response to carbon monoxide / regulation of GTPase activity ...regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of organ growth / response to antipsychotic drug / neurofilament cytoskeleton organization / myeloid cell homeostasis / peripheral nervous system myelin maintenance / response to superoxide / response to carbon monoxide / regulation of GTPase activity / auditory receptor cell stereocilium organization / anterograde axonal transport / protein phosphatase 2B binding / dense core granule / Oxidoreductases; Acting on a sulfur group of donors / retina homeostasis / hydrogen peroxide biosynthetic process / cellular response to potassium ion / muscle cell cellular homeostasis / retrograde axonal transport / superoxide metabolic process / heart contraction / response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / thymus development / superoxide dismutase activity / cellular response to cadmium ion / regulation of multicellular organism growth / relaxation of vascular associated smooth muscle / cellular response to ATP / response to axon injury / transmission of nerve impulse / reactive oxygen species metabolic process / placenta development / embryo implantation / sensory perception of sound / positive regulation of superoxide anion generation / response to amphetamine / removal of superoxide radicals / axon cytoplasm / ovarian follicle development / positive regulation of phagocytosis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / regulation of mitochondrial membrane potential / locomotory behavior / dendrite cytoplasm / glutathione metabolic process / response to hydrogen peroxide / positive regulation of cytokine production / regulation of blood pressure / negative regulation of inflammatory response / response to nutrient levels / mitochondrial intermembrane space / small GTPase binding / Platelet degranulation / peroxisome / negative regulation of neuron apoptotic process / response to heat / protein-folding chaperone binding / spermatogenesis / cytoplasmic vesicle / response to ethanol / intracellular iron ion homeostasis / : / positive regulation of MAPK cascade / lysosome / positive regulation of apoptotic process / mitochondrial matrix / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / zinc ion binding / nucleoplasm / extracellular region / 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: 2.95 Å
AuthorsWang LQ / Ma YY / Yuan HY / Zhao K / Zhang MY / Wang Q / Huang X / Xu WC / Chen J / Li D ...Wang LQ / Ma YY / Yuan HY / Zhao K / Zhang MY / Wang Q / Huang X / Xu WC / Chen J / Li D / Zhang DL / Zou LY / Yin P / Liu C / Liang Y
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770833 China
National Natural Science Foundation of China (NSFC)32071212 China
National Natural Science Foundation of China (NSFC)31570779 China
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structure of an amyloid fibril formed by full-length human SOD1 reveals its conformational conversion.
Authors: Li-Qiang Wang / Yeyang Ma / Han-Ye Yuan / Kun Zhao / Mu-Ya Zhang / Qiang Wang / Xi Huang / Wen-Chang Xu / Bin Dai / Jie Chen / Dan Li / Delin Zhang / Zhengzhi Wang / Liangyu Zou / Ping Yin / ...Authors: Li-Qiang Wang / Yeyang Ma / Han-Ye Yuan / Kun Zhao / Mu-Ya Zhang / Qiang Wang / Xi Huang / Wen-Chang Xu / Bin Dai / Jie Chen / Dan Li / Delin Zhang / Zhengzhi Wang / Liangyu Zou / Ping Yin / Cong Liu / Yi Liang /
Abstract: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease. Misfolded Cu, Zn-superoxide dismutase (SOD1) has been linked to both familial and sporadic ALS. SOD1 fibrils formed in vitro share ...Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease. Misfolded Cu, Zn-superoxide dismutase (SOD1) has been linked to both familial and sporadic ALS. SOD1 fibrils formed in vitro share toxic properties with ALS inclusions. Here we produced cytotoxic amyloid fibrils from full-length apo human SOD1 under reducing conditions and determined the atomic structure using cryo-EM. The SOD1 fibril consists of a single protofilament with a left-handed helix. The fibril core exhibits a serpentine fold comprising N-terminal segment (residues 3-55) and C-terminal segment (residues 86-153) with an intrinsic disordered segment. The two segments are zipped up by three salt bridge pairs. By comparison with the structure of apo SOD1 dimer, we propose that eight β-strands (to form a β-barrel) and one α-helix in the subunit of apo SOD1 convert into thirteen β-strands stabilized by five hydrophobic cavities in the SOD1 fibril. Our data provide insights into how SOD1 converts between structurally and functionally distinct states.
History
DepositionNov 16, 2021-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32227.png

Downloads & links

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Map

FileDownload / File: emd_32227.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe cryo-EM map of SOD1 fibril.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0187
Minimum - Maximum-0.05902609 - 0.09761211
Average (Standard dev.)0.0002369391 (±0.0023840163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human SOD1 amyloid fibril

EntireName: Human SOD1 amyloid fibril
Components
  • Organelle or cellular component: Human SOD1 amyloid fibril
    • Protein or peptide: Superoxide dismutase [Cu-Zn]

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Supramolecule #1: Human SOD1 amyloid fibril

SupramoleculeName: Human SOD1 amyloid fibril / 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: 15.958757 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MATKAVCVLK GDGPVQGIIN FEQKESNGPV KVWGSIKGLT EGLHGFHVHE FGDNTAGCTS AGPHFNPLSR KHGGPKDEER HVGDLGNVT 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 K2 SUMMIT (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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.82 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.187 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70067
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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