+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6482 | |||||||||
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Title | Cryo-electron microscopy of alpha Synuclein amyloid fibrils | |||||||||
Map data | Extruded 2D reconstruction of in vitro assembled alpha Synuclein amyoid fibrils | |||||||||
Sample |
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Function / homology | Function and homology information protein binding / 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 ...protein binding / 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 / fatty acid binding / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 40.0 Å | |||||||||
Authors | Dearborn AD / Wall JS / Cheng N / Heymann JB / Kajava AV / Varkey J / Langen R / Steven AC | |||||||||
Citation | Journal: J Biol Chem / Year: 2016 Title: α-Synuclein Amyloid Fibrils with Two Entwined, Asymmetrically Associated Protofibrils. Authors: Altaira D Dearborn / Joseph S Wall / Naiqian Cheng / J Bernard Heymann / Andrey V Kajava / Jobin Varkey / Ralf Langen / Alasdair C Steven / Abstract: Parkinson disease and other progressive neurodegenerative conditions are characterized by the intracerebral presence of Lewy bodies, containing amyloid fibrils of α-synuclein. We used cryo-electron ...Parkinson disease and other progressive neurodegenerative conditions are characterized by the intracerebral presence of Lewy bodies, containing amyloid fibrils of α-synuclein. We used cryo-electron microscopy and scanning transmission electron microscopy (STEM) to study in vitro-assembled fibrils. These fibrils are highly polymorphic. Focusing on twisting fibrils with an inter-crossover spacing of 77 nm, our reconstructions showed them to consist of paired protofibrils. STEM mass per length data gave one subunit per 0.47 nm axial rise per protofibril, consistent with a superpleated β-structure. The STEM images show two thread-like densities running along each of these fibrils, which we interpret as ladders of metal ions. These threads confirmed the two-protofibril architecture of the 77-nm twisting fibrils and allowed us to identify this morphotype in STEM micrographs. Some other, but not all, fibril morphotypes also exhibit dense threads, implying that they also present a putative metal binding site. We propose a molecular model for the protofibril and suggest that polymorphic variant fibrils have different numbers of protofibrils that are associated differently. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6482.map.gz | 13.8 MB | EMDB map data format | |
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Header (meta data) | emd-6482-v30.xml emd-6482.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_6482.png | 54.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6482 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6482 | HTTPS FTP |
-Validation report
Summary document | emd_6482_validation.pdf.gz | 79 KB | Display | EMDB validaton report |
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Full document | emd_6482_full_validation.pdf.gz | 78.1 KB | Display | |
Data in XML | emd_6482_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6482 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6482 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6482.map.gz / Format: CCP4 / Size: 14.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Extruded 2D reconstruction of in vitro assembled alpha Synuclein amyoid fibrils | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : In vitro assembled, recombinant amyloid fibrils of full-length hu...
Entire | Name: In vitro assembled, recombinant amyloid fibrils of full-length human alpha Synuclein |
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Components |
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-Supramolecule #1000: In vitro assembled, recombinant amyloid fibrils of full-length hu...
Supramolecule | Name: In vitro assembled, recombinant amyloid fibrils of full-length human alpha Synuclein type: sample / ID: 1000 / Details: The sample was morphologically heterogeneous. / Oligomeric state: dimeric asymmetric unit / Number unique components: 2 |
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Molecular weight | Method: Dark-field scanning transmission electron microscopy 59.1 MDa/micron compared to 61.5 MDa/micron theoretical weight |
-Macromolecule #1: alpha Synuclein
Macromolecule | Name: alpha Synuclein / type: protein_or_peptide / ID: 1 / Name.synonym: NACP, PARK1 / Oligomeric state: Amyloid / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: Brain / Cell: Neuron / Location in cell: Lewy Body |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21*(DE3)pLysS / Recombinant plasmid: pRK172aS |
Sequence | UniProtKB: Alpha-synuclein GO: magnesium ion binding, fatty acid binding, copper ion binding, calcium ion binding, protein binding InterPro: Alpha-synuclein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.4 / Details: 10 mM HEPES, 100 mM NaCl, 0.1% NaN3 |
Grid | Details: R1.2/1.3 400 mesh copper Quantifoil grid, glow-discharged in argon/oxygen |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 90 K / Instrument: LEICA KF80 / Method: Manually blotted before plunging |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Date | Jun 5, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 110 / Average electron dose: 15 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 51840 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The 2D reconstructions were made and aligned using bhelcross. The helical parameters were determined per fibril in real space and imposed on the average using bhelcross. |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.7 Å Applied symmetry - Helical parameters - Δ&Phi: 1.1 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: OTHER / Software - Name: Bsoft Details: Extruded from a 2D reconstruction based upon helical parameters |
CTF correction | Details: phase-flipped micrograph |