+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19446 | ||||||||||||
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Title | Alpha-synuclein amyloid fibrils | ||||||||||||
Map data | Postprocessed map of the alpha-synuclein amyloid fibril core | ||||||||||||
Sample |
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Keywords | Chaperones / amyloid fibril / 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 / regulation of norepinephrine uptake / response to iron(II) ion / 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 / dopamine uptake involved in synaptic transmission / synaptic vesicle transport / 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 / localization / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / excitatory postsynaptic potential / response to interleukin-1 / adult locomotory behavior / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / negative regulation of protein kinase activity / protein destabilization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / histone binding / cellular response to oxidative stress / growth cone / postsynapse / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / molecular adaptor activity / oxidoreductase activity / lysosome / transcription cis-regulatory region binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Saibil HR / Monistrol J | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Biorxiv / Year: 2024 Title: Stepwise recruitment of Hsc70 by DNAJB1 produces ordered arrays primed for bursts of amyloid fibre disassembly Authors: Monistrol J / Beton JG / Johnston EC / Saibil HR | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19446.map.gz | 16.7 MB | EMDB map data format | |
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Header (meta data) | emd-19446-v30.xml emd-19446.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19446_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_19446.png | 26.9 KB | ||
Masks | emd_19446_msk_1.map | 282.6 MB | Mask map | |
Filedesc metadata | emd-19446.cif.gz | 5.7 KB | ||
Others | emd_19446_half_map_1.map.gz emd_19446_half_map_2.map.gz | 223.3 MB 223.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19446 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19446 | HTTPS FTP |
-Validation report
Summary document | emd_19446_validation.pdf.gz | 625.9 KB | Display | EMDB validaton report |
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Full document | emd_19446_full_validation.pdf.gz | 625.5 KB | Display | |
Data in XML | emd_19446_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | emd_19446_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19446 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19446 | HTTPS FTP |
-Related structure data
Related structure data | 8rqmMC 8rrrC C: citing same article (ref.) M: atomic model generated by this map |
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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_19446.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Postprocessed map of the alpha-synuclein amyloid fibril core | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19446_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map #1 of the alpha-synuclein amyloid fibril core
File | emd_19446_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map #1 of the alpha-synuclein amyloid fibril core | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map #2 of the alpha-synuclein amyloid fibril core
File | emd_19446_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map #2 of the alpha-synuclein amyloid fibril core | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Alpha-synuclein amyloid fibril
Entire | Name: Alpha-synuclein amyloid fibril |
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Components |
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-Supramolecule #1: Alpha-synuclein amyloid fibril
Supramolecule | Name: Alpha-synuclein amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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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: 14.476108 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDVFMKGLSK AKEGVVAAAE KTKQGVAEAA GKTKEGVLYV GSKTKEGVVH GVATVAEKTK EQVTNVGGAV VTGVTAVAQK TVEGAGSIA AATGFVKKDQ LGKNEEGAPQ EGILEDMPVD PDNEAYEMPS EEGYQDYEPE A UniProtKB: Alpha-synuclein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |