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Yorodumi- EMDB-32227: Cryo-EM structure of amyloid fibril formed by full-length human SOD1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32227 | ||||||||||||
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Title | Cryo-EM structure of amyloid fibril formed by full-length human SOD1 | ||||||||||||
Map data | The cryo-EM map of SOD1 fibril. | ||||||||||||
Sample |
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Function / homology | Function and homology information action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide ...action potential initiation / neurofilament cytoskeleton organization / negative regulation of cholesterol biosynthetic process / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / superoxide anion generation / regulation of T cell differentiation in thymus / retina homeostasis / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / removal of superoxide radicals / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / dendrite cytoplasm / positive regulation of superoxide anion generation / thymus development / locomotory behavior / regulation of mitochondrial membrane potential / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.95 Å | ||||||||||||
Authors | Wang 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
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32227.map.gz | 9.6 MB | EMDB map data format | |
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Header (meta data) | emd-32227-v30.xml emd-32227.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32227_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_32227.png | 100.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32227 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32227 | HTTPS FTP |
-Related structure data
Related structure data | 7vzfMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32227.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The cryo-EM map of SOD1 fibril. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Human SOD1 amyloid fibril
Entire | Name: Human SOD1 amyloid fibril |
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Components |
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-Supramolecule #1: Human SOD1 amyloid fibril
Supramolecule | Name: Human SOD1 amyloid fibril / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Superoxide dismutase [Cu-Zn]
Macromolecule | Name: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: superoxide dismutase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.958757 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MATKAVCVLK GDGPVQGIIN FEQKESNGPV KVWGSIKGLT EGLHGFHVHE FGDNTAGCTS AGPHFNPLSR KHGGPKDEER HVGDLGNVT ADKDGVADVS IEDSVISLSG DHCIIGRTLV VHEKADDLGK GGNEESTKTG NAGSRLACGV IGIAQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |