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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
TitleMicroED structure of the segment, GVVHGVTTVA, from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56
Map data2mFo-dFc map covering multiple unit cells. Structure factors measured from micro electron diffraction (microED) methods.
Sample
  • Sample: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56
  • Protein or peptide: alpha synuclein residues 47-56
KeywordsAmyloid fibrils / alpha-synuclein / MicroED Crystallography / Parkinson's Disease / Peptide / familial mutation A53T
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of synaptic vesicle recycling / regulation of reactive oxygen species biosynthetic process / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of norepinephrine uptake / transporter regulator activity / regulation of locomotion / mitochondrial ATP synthesis coupled electron transport / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / negative regulation of microtubule polymerization / synaptic vesicle transport / positive regulation of receptor recycling / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / dynein complex binding / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / positive regulation of endocytosis / positive regulation of exocytosis / response to magnesium ion / synaptic vesicle exocytosis / enzyme inhibitor activity / kinesin binding / synaptic vesicle endocytosis / regulation of presynapse assembly / response to type II interferon / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / alpha-tubulin binding / supramolecular fiber organization / inclusion body / phospholipid metabolic process / cellular response to copper ion / axon terminus / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / negative regulation of protein kinase activity / excitatory postsynaptic potential / fatty acid metabolic process / phosphoprotein binding / protein tetramerization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / protein destabilization / PKR-mediated signaling / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / actin binding / growth cone / cell cortex / cellular response to oxidative stress / neuron apoptotic process / chemical synaptic transmission / molecular adaptor activity / negative regulation of neuron apoptotic process / response to lipopolysaccharide / histone binding / amyloid fibril formation / lysosome / oxidoreductase activity / postsynapse / transcription cis-regulatory region binding / positive regulation of apoptotic process / Amyloid fiber formation / copper ion binding / response to xenobiotic stimulus / axon / neuronal cell body
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodelectron crystallography / cryo EM / Resolution: 1.4 Å
AuthorsRodriguez 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
CitationJournal: Nature / Year: 2015
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
DepositionMay 8, 2015-
Header (metadata) releaseMay 20, 2015-
Map releaseSep 9, 2015-
UpdateOct 7, 2015-
Current statusOct 7, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4znn
  • Surface level: 0.16
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3001.png

Downloads & links

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Map

FileDownload / File: emd_3001.map.gz / Format: CCP4 / Size: 300.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2mFo-dFc map covering multiple unit cells. Structure factors measured from micro electron diffraction (microED) methods.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
0.39 Å/pix.
x 25 pix.
= 4.71 Å		0.45 Å/pix.
x 43 pix.
= 17.93 Å		0.46 Å/pix.
x 73 pix.
= 33.03 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.44825 Å / Y: 0.3925 Å / Z: 0.45875 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.15 / Movie #1: 0.16
Minimum - Maximum-0.36814296 - 0.72161025
Average (Standard dev.)0.00053297 (±0.15705723)
SymmetrySpace group: 4
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-210-12
Dimensions437325
Spacing124072
CellA: 17.93 Å / B: 4.71 Å / C: 33.03 Å
α: 90.0 ° / β: 94.326 ° / γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.448250.39250.45875
M x/y/z401272
origin x/y/z0.0000.0000.000
length x/y/z17.9304.71033.030
α/β/γ90.00094.32690.000
start NX/NY/NZ-21-120
NX/NY/NZ432573
MAP C/R/S312
start NC/NR/NS0-21-12
NC/NR/NS734325
D min/max/mean-0.3680.7220.001

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Supplemental data

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Sample components

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Entire : GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson'...

EntireName: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56
Components
  • Sample: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56
  • Protein or peptide: alpha synuclein residues 47-56

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Supramolecule #1000: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson'...

SupramoleculeName: 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

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

Concentration5 mg/mL
BufferpH: 7 / Details: 50 mM phosphate, 0.1% w/v DMSO
GridDetails: quantifoil holey-carbon EM grid, 300 mesh copper
VitrificationCryogen 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.
DetailsCrystals grew in batch. In a microcentrifuge tube at 37 degrees C with shaking.
Crystal formationDetails: Crystals grew in batch. In a microcentrifuge tube at 37 degrees C with shaking.

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 99 K / Max: 101 K / Average: 100 K
Detailsvery low dose data collection. Spot size 11.
DateApr 20, 2015
Image recordingCategory: 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 beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: DIFFRACTION
Sample stageSpecimen 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

DetailsDiffraction 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.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.4 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Details: The diffraction data set contains intensities measured from three crystals.
Crystal parametersUnit 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

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