|Entry||Database: PDB / ID: 6a6b|
|Title||cryo-em structure of alpha-synuclein fiber|
|Keywords||PROTEIN FIBRIL / alpha-syn fiber / Parkinson disease|
|Function / homology||Alpha-synuclein / Synuclein / Amyloid fiber formation / Synuclein / negative regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of norepinephrine uptake / negative regulation of dopamine uptake involved in synaptic transmission / regulation of acyl-CoA biosynthetic process / positive regulation of glutathione peroxidase activity / regulation of phospholipase activity ...Alpha-synuclein / Synuclein / Amyloid fiber formation / Synuclein / negative regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of norepinephrine uptake / negative regulation of dopamine uptake involved in synaptic transmission / regulation of acyl-CoA biosynthetic process / positive regulation of glutathione peroxidase activity / regulation of phospholipase activity / neutral lipid metabolic process / response to desipramine / negative regulation of monooxygenase activity / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of chaperone-mediated autophagy / regulation of glutamate secretion / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / negative regulation of transporter activity / regulation of norepinephrine uptake / regulation of synaptic vesicle recycling / regulation of locomotion / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of inositol phosphate biosynthetic process / negative regulation of exocytosis / response to iron(II) ion / synaptic vesicle transport / positive regulation of neurotransmitter secretion / negative regulation of serotonin uptake / mitochondrial ATP synthesis coupled electron transport / dopamine biosynthetic process / negative regulation of histone acetylation / positive regulation of receptor recycling / negative regulation of microtubule polymerization / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / nuclear outer membrane / regulation of macrophage activation / negative regulation of dopamine metabolic process / dynein complex binding / beta-tubulin binding / alpha-tubulin binding / supramolecular fiber organization / phospholipase binding / synaptic vesicle endocytosis / kinesin binding / response to magnesium ion / positive regulation of endocytosis / cellular response to copper ion / response to interferon-gamma / negative regulation of thrombin-activated receptor signaling pathway / cellular response to fibroblast growth factor stimulus / cuprous ion binding / regulation of presynapse assembly / excitatory postsynaptic potential / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to interleukin-1 / behavioral response to cocaine / long-term synaptic potentiation / microglial cell activation / inclusion body / fatty acid metabolic process / regulation of transmembrane transporter activity / synapse organization / adult locomotory behavior / phospholipid metabolic process / cellular response to epinephrine stimulus / Hsp70 protein binding / tau protein binding / positive regulation of protein serine/threonine kinase activity / ferrous iron binding / rough endoplasmic reticulum / receptor internalization / regulation of long-term neuronal synaptic plasticity / synaptic vesicle membrane / negative regulation of protein phosphorylation / positive regulation of release of sequestered calcium ion into cytosol / terminal bouton / protein destabilization / negative regulation of neuron death / phospholipid binding / positive regulation of inflammatory response / phosphoprotein binding / postsynapse / mitochondrial intermembrane space / actin cytoskeleton / activation of cysteine-type endopeptidase activity involved in apoptotic process / cell cortex / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron death / cellular response to oxidative stress / growth cone / mitochondrial inner membrane / actin binding / histone binding / lysosome / transcription regulatory region DNA binding / protein N-terminus binding / positive regulation of peptidyl-serine phosphorylation|
Function and homology information
|Specimen source||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.07 Å resolution|
|Authors||Li, Y.W. / Zhao, C.Y. / Luo, F. / Liu, Z. / Gui, X. / Luo, Z. / Zhang, X. / Li, D. / Liu, C. / Li, X.|
|Citation||Journal: Cell Res. / Year: 2018|
Title: Amyloid fibril structure of α-synuclein determined by cryo-electron microscopy.
Authors: Yaowang Li / Chunyu Zhao / Feng Luo / Zhenying Liu / Xinrui Gui / Zhipu Luo / Xiang Zhang / Dan Li / Cong Liu / Xueming Li
SummaryFull reportAbout validation report
|Date||Deposition: Jun 27, 2018 / Release: Jul 11, 2018|
|Structure viewer||Molecule: |
Downloads & links
Mass: 6251.097 Da / Num. of mol.: 12 / Fragment: UNP residues 37-99 / Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P37840
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: helical reconstruction|
|Component||Name: alpha-synuclein fiber / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Source (natural)||Organism: Homo sapiens (human)|
|Source (recombinant)||Organism: Escherichia coli K-12 (bacteria)|
|Buffer solution||pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: 4 microl of alpha-syn fibril solution was applied to a glow-discharged holey carbon grid (Quantifoil R1.2/1.3, 300 mesh), blotted for 6 s, and plunge-frozen in liquid ethane using FEI Vitrobot Mark IV. 95% humidity, 16 degrees|
Grid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 289 kelvins|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Average exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|Image scans||Movie frames/image: 32 / Used frames/image: 1-32|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: 179.641 deg. / Axial rise/subunit: 2.393 Å / Axial symmetry: C1|
|3D reconstruction||Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 43677 / Symmetry type: HELICAL|
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