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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


regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / 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 ...regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / 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 / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / regulation of synaptic vesicle recycling / 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 / 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 / dynein complex binding / dopamine uptake involved in synaptic transmission / positive regulation of receptor recycling / regulation of dopamine secretion / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / response to magnesium ion / response to type II interferon / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrial ATP synthesis coupled electron transport / 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 / 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 / protein destabilization / negative regulation of protein kinase activity / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / positive regulation of protein serine/threonine kinase activity / tau protein binding / PKR-mediated signaling / receptor internalization / : / phospholipid binding / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / actin binding / cell cortex / cellular response to oxidative stress / histone binding / growth cone / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynapse / response to lipopolysaccharide / amyloid fibril formation / molecular adaptor activity / lysosome / transcription cis-regulatory region binding / oxidoreductase activity / positive regulation of apoptotic process
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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