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- EMDB-3001: MicroED structure of the segment, GVVHGVTTVA, from the A53T famil... -
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Basic information
Entry | Database: EMDB / ID: EMD-3001 | |||||||||
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Title | MicroED structure of the segment, GVVHGVTTVA, from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56 | |||||||||
![]() | 2mFo-dFc map covering multiple unit cells. Structure factors measured from micro electron diffraction (microED) methods. | |||||||||
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![]() | Amyloid fibrils / alpha-synuclein / MicroED Crystallography / Parkinson's Disease / Peptide / familial mutation A53T | |||||||||
Function / homology | ![]() 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 / regulation of dopamine secretion / positive regulation of receptor recycling / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / mitochondrial ATP synthesis coupled electron transport / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / synaptic vesicle endocytosis / regulation of presynapse assembly / 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 / positive regulation of protein serine/threonine kinase activity / PKR-mediated signaling / 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 / cellular response to oxidative stress / histone binding / cell cortex / growth cone / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynapse / 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 | ![]() | |||||||||
Method | electron crystallography / cryo EM / Resolution: 1.4 Å | |||||||||
![]() | Rodriguez JA / Ivanova M / Sawaya MR / Cascio D / Reyes F / Shi D / Johnson L / Guenther E / Sangwan S / Hattne J ...Rodriguez JA / Ivanova M / Sawaya MR / Cascio D / Reyes F / Shi D / Johnson L / Guenther E / Sangwan S / Hattne J / Nannenga B / Gonen T / Eisenberg D | |||||||||
![]() | ![]() Title: Structure of the toxic core of α-synuclein from invisible crystals. Authors: Jose A Rodriguez / Magdalena I Ivanova / Michael R Sawaya / Duilio Cascio / Francis E Reyes / Dan Shi / Smriti Sangwan / Elizabeth L Guenther / Lisa M Johnson / Meng Zhang / Lin Jiang / Mark ...Authors: Jose A Rodriguez / Magdalena I Ivanova / Michael R Sawaya / Duilio Cascio / Francis E Reyes / Dan Shi / Smriti Sangwan / Elizabeth L Guenther / Lisa M Johnson / Meng Zhang / Lin Jiang / Mark A Arbing / Brent L Nannenga / Johan Hattne / Julian Whitelegge / Aaron S Brewster / Marc Messerschmidt / Sébastien Boutet / Nicholas K Sauter / Tamir Gonen / David S Eisenberg / ![]() Abstract: The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term ...The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 263.8 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.2 KB 12.2 KB | Display Display | ![]() |
Images | ![]() | 399 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4znnMC ![]() 3028C ![]() 4rikC ![]() 4rilC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 2mFo-dFc map covering multiple unit cells. Structure factors measured from micro electron diffraction (microED) methods. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.44825 Å / Y: 0.3925 Å / Z: 0.45875 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson'...
Entire | Name: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56 |
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Components |
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-Supramolecule #1000: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson'...
Supramolecule | Name: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56 type: sample / ID: 1000 / Details: crystalline fibrils / Oligomeric state: crystalline fibrils / Number unique components: 1 |
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-Macromolecule #1: alpha synuclein residues 47-56
Macromolecule | Name: alpha synuclein residues 47-56 / type: protein_or_peptide / ID: 1 / Name.synonym: a-syn Details: alpha synuclein residues 47-56 with A53T mutation. Synthesized chemically. Number of copies: 1 / Oligomeric state: fibril / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron crystallography |
Aggregation state | 3D array |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7 / Details: 50 mM phosphate, 0.1% w/v DMSO |
Grid | Details: quantifoil holey-carbon EM grid, 300 mesh copper |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV Method: Nanocrystals were deposited onto a quantifoil holey-carbon EM grid in a 2-3 microliter drop after appropriate dilution, which optimized for crystal density on the grid. All grids were then ...Method: Nanocrystals were deposited onto a quantifoil holey-carbon EM grid in a 2-3 microliter drop after appropriate dilution, which optimized for crystal density on the grid. All grids were then blotted and vitrified by plunging into liquid ethane using a Vitrobot Mark IV (FEI), then transferring to liquid nitrogen for storage. |
Details | Crystals grew in batch. In a microcentrifuge tube at 37 degrees C with shaking. |
Crystal formation | Details: Crystals grew in batch. In a microcentrifuge tube at 37 degrees C with shaking. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 99 K / Max: 101 K / Average: 100 K |
Details | very low dose data collection. Spot size 11. |
Date | Apr 20, 2015 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 343 / Average electron dose: 0.10000000000000001 e/Å2 / Camera length: 2230 / Details: Diffraction images are available upon request. / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION |
Sample stage | Specimen holder: liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle min: -66 / Tilt angle max: 66 / Tilt series - Axis1 - Min angle: -66 ° / Tilt series - Axis1 - Max angle: 66 ° |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Details | Diffraction images were processed with XDS and XSCALE. Please note that the unit cell length B is 4.71 A. This value was not accepted as valid on the web submission page. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 1.4 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES Details: The diffraction data set contains intensities measured from three crystals. |
Crystal parameters | Unit cell - A: 17.930 Å / Unit cell - B: 4.71 Å / Unit cell - C: 33.030 Å / Unit cell - γ: 90.0 ° / Unit cell - α: 90 ° / Unit cell - β: 94.33 ° / Space group: P 1 21 1 |