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- PDB-9iyd: Cryo-EM structure of an amyloid fibril formed by SOD1 mutant - G93A -

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Basic information

Entry
Database: PDB / ID: 9iyd
TitleCryo-EM structure of an amyloid fibril formed by SOD1 mutant - G93A
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsPROTEIN FIBRIL / Amyloid fibril
Function / homology
Function and homology information


regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / regulation of organ growth / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide ...regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / regulation of organ growth / relaxation of vascular associated smooth muscle / peripheral nervous system myelin maintenance / response to carbon monoxide / response to superoxide / regulation of GTPase activity / myeloid cell homeostasis / anterograde axonal transport / protein phosphatase 2B binding / dense core granule / Oxidoreductases; Acting on a sulfur group of donors / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / muscle cell cellular homeostasis / cellular response to potassium ion / superoxide anion generation / retrograde axonal transport / superoxide metabolic process / heart contraction / response to copper ion / superoxide dismutase / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to cadmium ion / regulation of multicellular organism growth / negative regulation of reproductive process / negative regulation of developmental process / ectopic germ cell programmed cell death / cellular response to ATP / transmission of nerve impulse / response to axon injury / ovarian follicle development / thymus development / neuronal action potential / embryo implantation / determination of adult lifespan / positive regulation of superoxide anion generation / reactive oxygen species metabolic process / axon cytoplasm / removal of superoxide radicals / placenta development / sensory perception of sound / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of phagocytosis / response to amphetamine / dendrite cytoplasm / regulation of mitochondrial membrane potential / positive regulation of cytokine production / glutathione metabolic process / locomotory behavior / response to hydrogen peroxide / negative regulation of inflammatory response / response to nutrient levels / mitochondrial intermembrane space / regulation of blood pressure / small GTPase binding / gene expression / Platelet degranulation / peroxisome / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / negative regulation of neuron apoptotic process / response to ethanol / intracellular iron ion homeostasis / positive regulation of MAPK cascade / lysosome / response to xenobiotic stimulus / positive regulation of apoptotic process / mitochondrial matrix / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / : / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsZhang, M.Y. / Ma, Y.Y. / Wang, L.Q. / Xia, W.C. / Yuan, H.Y. / Zhao, K. / Chen, J. / Li, D. / Zou, L.Y. / Wang, Z.Z. ...Zhang, M.Y. / Ma, Y.Y. / Wang, L.Q. / Xia, W.C. / Yuan, H.Y. / Zhao, K. / Chen, J. / Li, D. / Zou, L.Y. / Wang, Z.Z. / Liu, C. / Liang, Y.
Funding support China, 4items
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: EMBO Rep / Year: 2025
Title: Distinct amyloid fibril structures formed by ALS-causing SOD1 mutants G93A and D101N.
Authors: Mu-Ya Zhang / Yeyang Ma / Li-Qiang Wang / Wencheng Xia / Xiang-Ning Li / Kun Zhao / Jie Chen / Dan Li / Liangyu Zou / Zhengzhi Wang / Cong Liu / Yi Liang /
Abstract: Two hundred eight genetic mutations in SOD1 have been linked to amyotrophic lateral sclerosis (ALS). Of these, the G93A and D101N variants maintain much of their physiological function, closely ...Two hundred eight genetic mutations in SOD1 have been linked to amyotrophic lateral sclerosis (ALS). Of these, the G93A and D101N variants maintain much of their physiological function, closely resembling that of wild-type SOD1, and the SOD1-G93A transgenic mouse is the most extensively used mouse line in the study of ALS. In this study, we report two cryo-EM structures of amyloid fibrils formed by G93A and D101N mutants of SOD1 protein. These mutations give rise to amyloid fibrils with distinct structures compared to native SOD1 fibrils. The fibril core displays a serpentine configuration featuring four β-strands, held together by two hydrophobic cavities and a salt bridge between Arg143 and Asp96 in the G93A fibril, and by a hydrophobic cavity and a salt bridge between Arg143 and Asp132 in the D101N fibril, demonstrating unique structural features for each mutant. Moreover, our results show that G93A fibrils are significantly more toxic than those formed by D101N, which do not show a marked increase in toxicity compared to wild-type SOD1 fibrils. This study sheds light on the structural mechanisms through which SOD1 mutants aggregate and induce cytotoxicity in ALS.
History
DepositionJul 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]


Theoretical massNumber of molelcules
Total (without water)47,9183
Polymers47,9183
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Superoxide dismutase [Cu-Zn] / Superoxide dismutase 1 / hSod1


Mass: 15972.782 Da / Num. of mol.: 3 / Mutation: G94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: ALS-causing SOD1 mutant G93A / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.15.2_3472: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.73 ° / Axial rise/subunit: 4.88 Å / Axial symmetry: C1
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57507 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0081512
ELECTRON MICROSCOPYf_angle_d0.9122037
ELECTRON MICROSCOPYf_dihedral_angle_d3.783903
ELECTRON MICROSCOPYf_chiral_restr0.054249
ELECTRON MICROSCOPYf_plane_restr0.004273

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