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- PDB-9jbp: Cryo-EM structure of human SOD1 (C6A/C111A) amyloid filament -

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Basic information

Entry
Database: PDB / ID: 9jbp
TitleCryo-EM structure of human SOD1 (C6A/C111A) amyloid filament
Components
  • Superoxide dismutase [Cu-Zn]
  • Unassigned poly-alanine model
KeywordsPROTEIN FIBRIL / amyloid / filament / superoxide dismutase 1 / amyotrophic lateral sclerosis
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsBaek, Y. / Kim, H. / Lee, D. / Kim, D. / Jo, E. / Roh, S.-H. / Ha, N.-C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural insights into the role of reduced cysteine residues in SOD1 amyloid filament formation.
Authors: Yeongjin Baek / Hyunmin Kim / Dukwon Lee / Doyeon Kim / Eunbyul Jo / Soung-Hun Roh / Nam-Chul Ha /
Abstract: The formation of superoxide dismutase 1 (SOD1) filaments has been implicated in amyotrophic lateral sclerosis (ALS). Although the disulfide bond formed between Cys57 and Cys146 in the active state ...The formation of superoxide dismutase 1 (SOD1) filaments has been implicated in amyotrophic lateral sclerosis (ALS). Although the disulfide bond formed between Cys57 and Cys146 in the active state has been well studied, the role of the reduced cysteine residues, Cys6 and Cys111, in SOD1 filament formation remains unclear. In this study, we investigated the role of reduced cysteine residues by determining and comparing cryoelectron microscopy (cryo-EM) structures of wild-type (WT) and C6A/C111A SOD1 filaments under thiol-based reducing and metal-depriving conditions, starting with protein samples possessing enzymatic activity. The C6A/C111A mutant SOD1 formed filaments more rapidly than the WT protein. The mutant structure had a unique paired-protofilament arrangement, with a smaller filament core than that of the single-protofilament structure observed in WT SOD1. Although the single-protofilament form developed more slowly, cross-seeding experiments demonstrated the predominance of single-protofilament morphology over paired protofilaments, regardless of the presence of the Cys6 and Cys111 mutations. These findings highlight the importance of the number of amino acid residues within the filament core in determining the energy requirements for assembly. Our study provides insights into ALS pathogenesis by elucidating the initiation and propagation of filament formation, which potentially leads to deleterious amyloid filaments.
History
DepositionAug 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
G: Unassigned poly-alanine model
B: Superoxide dismutase [Cu-Zn]
H: Unassigned poly-alanine model
C: Superoxide dismutase [Cu-Zn]
I: Unassigned poly-alanine model
D: Superoxide dismutase [Cu-Zn]
J: Unassigned poly-alanine model
E: Superoxide dismutase [Cu-Zn]
K: Unassigned poly-alanine model
F: Superoxide dismutase [Cu-Zn]
L: Unassigned poly-alanine model


Theoretical massNumber of molelcules
Total (without water)104,04812
Polymers104,04812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, amyloid filaments are shown in EM images
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 16642.439 Da / Num. of mol.: 6 / Mutation: C6A,C111A
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
#2: Protein/peptide
Unassigned poly-alanine model


Mass: 698.854 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: superoxide dismutase[Cu-Zn](P00441) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: Amyloid filament of human C6A/C111A mutant SOD1 protein
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 69.6 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1782

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1RELION4particle selectionstart-end manual picking
4RELION4CTF correctionCTFFIND-4.1
7Cootmodel fitting
9PHENIX1.21model refinement
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.602 ° / Axial rise/subunit: 2.397 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 973528
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 679265 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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