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Yorodumi- EMDB-29980: Cryo-EM structure of serine 87 O-GlcNAc-modified alpha-synuclein ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29980 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of serine 87 O-GlcNAc-modified alpha-synuclein fibrils | ||||||||||||||||||||||||
Map data | main map. This map was used to build model | ||||||||||||||||||||||||
Sample |
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Keywords | alpha-synuclein / O-GlcNAc / amyloid / fibril / posttranslational modification / PROTEIN FIBRIL | ||||||||||||||||||||||||
Function / homology | Function and homology information negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / regulation of norepinephrine uptake / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / synaptic vesicle transport / dopamine uptake involved in synaptic transmission / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / synaptic vesicle exocytosis / positive regulation of exocytosis / kinesin binding / positive regulation of endocytosis / mitochondrial ATP synthesis coupled electron transport / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / regulation of presynapse assembly / synaptic vesicle endocytosis / negative regulation of serotonin uptake / alpha-tubulin binding / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / adult locomotory behavior / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / synapse organization / microglial cell activation / negative regulation of protein kinase activity / regulation of long-term neuronal synaptic plasticity / protein destabilization / ferrous iron binding / tau protein binding / PKR-mediated signaling / positive regulation of protein serine/threonine kinase activity / receptor internalization / phospholipid binding / synaptic vesicle membrane / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / actin binding / cell cortex / cellular response to oxidative stress / histone binding / growth cone / chemical synaptic transmission / neuron apoptotic process / postsynapse / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / molecular adaptor activity / oxidoreductase activity / lysosome / transcription cis-regulatory region binding / response to xenobiotic stimulus Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||||||||||||||
Authors | Balana JA / Nguyen AB / Saelices L / Pratt RM | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology. Authors: Aaron T Balana / Anne-Laure Mahul-Mellier / Binh A Nguyen / Mian Horvath / Afraah Javed / Eldon R Hard / Yllza Jasiqi / Preeti Singh / Shumaila Afrin / Rose Pedretti / Virender Singh / ...Authors: Aaron T Balana / Anne-Laure Mahul-Mellier / Binh A Nguyen / Mian Horvath / Afraah Javed / Eldon R Hard / Yllza Jasiqi / Preeti Singh / Shumaila Afrin / Rose Pedretti / Virender Singh / Virginia M-Y Lee / Kelvin C Luk / Lorena Saelices / Hilal A Lashuel / Matthew R Pratt / Abstract: Amyloid-forming proteins such α-synuclein and tau, which are implicated in Alzheimer's and Parkinson's disease, can form different fibril structures or strains with distinct toxic properties, ...Amyloid-forming proteins such α-synuclein and tau, which are implicated in Alzheimer's and Parkinson's disease, can form different fibril structures or strains with distinct toxic properties, seeding activities and pathology. Understanding the determinants contributing to the formation of different amyloid features could open new avenues for developing disease-specific diagnostics and therapies. Here we report that O-GlcNAc modification of α-synuclein monomers results in the formation of amyloid fibril with distinct core structure, as revealed by cryogenic electron microscopy, and diminished seeding activity in seeding-based neuronal and rodent models of Parkinson's disease. Although the mechanisms underpinning the seeding neutralization activity of the O-GlcNAc-modified fibrils remain unclear, our in vitro mechanistic studies indicate that heat shock proteins interactions with O-GlcNAc fibril inhibit their seeding activity, suggesting that the O-GlcNAc modification may alter the interactome of the α-synuclein fibrils in ways that lead to reduce seeding activity in vivo. Our results show that posttranslational modifications, such as O-GlcNAc modification, of α-synuclein are key determinants of α-synuclein amyloid strains and pathogenicity. | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29980.map.gz | 60.6 MB | EMDB map data format | |
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Header (meta data) | emd-29980-v30.xml emd-29980.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29980_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_29980.png | 61.3 KB | ||
Masks | emd_29980_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-29980.cif.gz | 5.7 KB | ||
Others | emd_29980_additional_1.map.gz emd_29980_half_map_1.map.gz emd_29980_half_map_2.map.gz | 97.9 MB 98.1 MB 98.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29980 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29980 | HTTPS FTP |
-Validation report
Summary document | emd_29980_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_29980_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_29980_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_29980_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29980 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29980 | HTTPS FTP |
-Related structure data
Related structure data | 8gf7MC 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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-Map
File | Download / File: emd_29980.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main map. This map was used to build model | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29980_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: this map was reconstructed from 3Drefine step in RELION
File | emd_29980_additional_1.map | ||||||||||||
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Annotation | this map was reconstructed from 3Drefine step in RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_29980_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_29980_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : alpha-synuclein fibrils
Entire | Name: alpha-synuclein fibrils |
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Components |
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-Supramolecule #1: alpha-synuclein fibrils
Supramolecule | Name: alpha-synuclein fibrils / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: The protein is semi-synthesized. |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Alpha-synuclein
Macromolecule | Name: Alpha-synuclein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.781005 KDa |
Sequence | String: GLSKAKEGVV AAAEKTKQGV AEAAGKTKEG VLYVGSKTKE GVVHGVATVA EKTKEQVTNV GGAVVTGVTA VAQKTVEGAG SIAAATGFV K UniProtKB: Alpha-synuclein |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 / Details: normal PBS |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 7270 / Average exposure time: 3.6 sec. / Average electron dose: 40.0 e/Å2 / Details: 3 shots per hole |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |