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- PDB-6a6b: cryo-em structure of alpha-synuclein fiber -

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Basic information

Entry
Database: PDB / ID: 6a6b
Titlecryo-em structure of alpha-synuclein fiber
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / alpha-syn fiber / Parkinson disease
Function / homologyAmyloid fiber formation / Synuclein / Alpha-synuclein / Synuclein / negative regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of norepinephrine uptake / neutral lipid metabolic process / response to desipramine / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of monooxygenase activity ...Amyloid fiber formation / Synuclein / Alpha-synuclein / Synuclein / negative regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of norepinephrine uptake / neutral lipid metabolic process / response to desipramine / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of monooxygenase activity / regulation of phospholipase activity / positive regulation of glutathione peroxidase activity / regulation of acyl-CoA biosynthetic process / positive regulation of hydrogen peroxide catabolic process / mitochondrial membrane organization / supramolecular fiber / regulation of glutamate secretion / regulation of reactive oxygen species biosynthetic process / negative regulation of transporter activity / regulation of presynapse assembly / negative regulation of chaperone-mediated autophagy / regulation of norepinephrine uptake / regulation of locomotion / regulation of synaptic vesicle recycling / 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 / positive regulation of neurotransmitter secretion / negative regulation of serotonin uptake / dopamine biosynthetic process / mitochondrial ATP synthesis coupled electron transport / negative regulation of histone acetylation / synaptic vesicle transport / positive regulation of receptor recycling / negative regulation of microtubule polymerization / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / nuclear outer membrane / synaptic vesicle endocytosis / regulation of macrophage activation / negative regulation of dopamine metabolic process / dynein complex binding / beta-tubulin binding / supramolecular fiber organization / alpha-tubulin binding / phospholipase binding / positive regulation of endocytosis / kinesin binding / response to magnesium ion / 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 / excitatory postsynaptic potential / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to interleukin-1 / behavioral response to cocaine / microglial cell activation / inclusion body / long-term synaptic potentiation / fatty acid metabolic process / regulation of transmembrane transporter activity / Hsp70 protein binding / synapse organization / adult locomotory behavior / phospholipid metabolic process / cellular response to epinephrine stimulus / postsynapse / tau protein binding / synaptic vesicle / ferrous iron binding / positive regulation of protein serine/threonine kinase activity / rough endoplasmic reticulum / negative regulation of protein phosphorylation / regulation of long-term neuronal synaptic plasticity / receptor internalization / positive regulation of release of sequestered calcium ion into cytosol / terminal bouton / protein destabilization / negative regulation of neuron death / phospholipid binding / cytoplasmic vesicle membrane / positive regulation of inflammatory response / phosphoprotein binding / mitochondrial intermembrane space / actin cytoskeleton / activation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell cortex / positive regulation of neuron death / growth cone / cellular response to oxidative stress / mitochondrial inner membrane / actin binding / histone binding / transcription regulatory region DNA binding / lysosome / ribosome
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.07 Å resolution
AuthorsLi, Y.W. / Zhao, C.Y. / Luo, F. / Liu, Z. / Gui, X. / Luo, Z. / Zhang, X. / Li, D. / Liu, C. / Li, X.
CitationJournal: To Be Published
Title: cryo-em structure of alpha-synuclein fiber
Authors: Li, Y.W. / Zhao, C.Y. / Luo, F. / Liu, Z. / Gui, X. / Luo, Z. / Zhang, X. / Li, D. / Liu, C. / Li, X.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 27, 2018 / Release: Jul 11, 2018
RevisionDateData content typeGroupCategoryProviderType
1.0Jul 11, 2018Structure modelrepositoryInitial release
1.1Aug 1, 2018Structure modelData collection / Derived calculationspdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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Structure visualization

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  • Biological unit as assembly
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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Alpha-synuclein
B: Alpha-synuclein
C: Alpha-synuclein
D: Alpha-synuclein
E: Alpha-synuclein
F: Alpha-synuclein
G: Alpha-synuclein
H: Alpha-synuclein
I: Alpha-synuclein
J: Alpha-synuclein
K: Alpha-synuclein
L: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)75,01312
Polyers75,01312
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy, TEM, AFM and x-ray diffraction
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)50960
ΔGint (kcal/M)-185
Surface area (Å2)26990

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Components

#1: Protein/peptide
Alpha-synuclein / / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: 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 solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 289 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 32 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategory
4CTFFIND4CTF correction
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.641 deg. / Axial rise/subunit: 2.393 Å / Axial symmetry: C1
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 43677 / Symmetry type: HELICAL

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