|Entry||Database: PDB / ID: 6flt|
|Title||Structure of alpha-synuclein fibrils|
|Keywords||PROTEIN FIBRIL / Parkinson's disease / apha-synuclein / fibril / filament|
|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 / negative regulation of exocytosis / positive regulation of inositol phosphate biosynthetic process / response to iron(II) ion / positive regulation of neurotransmitter secretion / negative regulation of serotonin uptake / mitochondrial ATP synthesis coupled electron transport / dopamine biosynthetic process / synaptic vesicle transport / 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 / kinesin binding / response to magnesium ion / positive regulation of endocytosis / synaptic vesicle endocytosis / 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 / regulation of transmembrane transporter activity / synapse organization / adult locomotory behavior / phospholipid metabolic process / cellular response to epinephrine stimulus / Hsp70 protein binding / tau protein binding / fatty acid metabolic process / positive regulation of protein serine/threonine kinase activity / ferrous iron binding / rough endoplasmic reticulum / receptor internalization / regulation of long-term neuronal synaptic plasticity / negative regulation of protein phosphorylation / synaptic vesicle membrane / positive regulation of release of sequestered calcium ion into cytosol / terminal bouton / cellular response to copper ion / 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 / histone binding / mitochondrial inner membrane / actin 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 / 3.42 Å resolution|
|Authors||Guerrero-Ferreira, R. / Taylor, N.M.I. / Mona, D. / Riek, R. / Britschgi, M. / Stahlberg, H.|
|Citation||Journal: Elife / Year: 2018|
Title: Cryo-EM structure of alpha-synuclein fibrils.
Authors: Ricardo Guerrero-Ferreira / Nicholas Mi Taylor / Daniel Mona / Philippe Ringler / Matthias E Lauer / Roland Riek / Markus Britschgi / Henning Stahlberg
Abstract: Parkinson's disease is a progressive neuropathological disorder that belongs to the class of synucleinopathies, in which the protein alpha-synuclein is found at abnormally high concentrations in ...Parkinson's disease is a progressive neuropathological disorder that belongs to the class of synucleinopathies, in which the protein alpha-synuclein is found at abnormally high concentrations in affected neurons. Its hallmark are intracellular inclusions called Lewy bodies and Lewy neurites. We here report the structure of cytotoxic alpha-synuclein fibrils (residues 1-121), determined by cryo-electron microscopy at a resolution of 3.4 Å. Two protofilaments form a polar fibril composed of staggered β-strands. The backbone of residues 38 to 95, including the fibril core and the non-amyloid component region, are well resolved in the EM map. Residues 50-57, containing three of the mutation sites associated with familial synucleinopathies, form the interface between the two protofilaments and contribute to fibril stability. A hydrophobic cleft at one end of the fibril may have implications for fibril elongation, and invites for the design of molecules for diagnosis and treatment of synucleinopathies.
SummaryFull reportAbout validation report
|Date||Deposition: Jan 28, 2018 / Release: Jun 27, 2018|
|Structure viewer||Molecule: |
Downloads & links
Mass: 12242.873 Da / Num. of mol.: 10 / Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Plasmid name: pET21
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P37840
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: helical reconstruction|
|Component||Name: Alpha-synuclein fibrils / Type: COMPLEX / Details: Residues 1-121 / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Homo sapiens (human)|
|Source (recombinant)||Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)|
|Buffer solution||pH: 7.3|
|Specimen||Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/2|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 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||Electron dose: 100 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|EM imaging optics||Energyfilter name: GIF Quantum LS|
|Image scans||Movie frames/image: 50 / Used frames/image: 2-50|
|Software||Name: PHENIX / Version: 1.13_2998: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: -179.5 deg. / Axial rise/subunit: 2.45 Å / Axial symmetry: C1|
|Particle selection||Details: Segments extracted from 792 manually picked fibrils|
Number of particles selected: 18860
|3D reconstruction||Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 13390 / Symmetry type: POINT|
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi