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- EMDB-6988: cryo-em structure of alpha-synuclein fiber -

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Basic information

Entry
Database: EMDB / ID: 6988
Titlecryo-em structure of alpha-synuclein fiber
Map dataDensity map calculated by applying a helical symmetry to the segments in the middle of 3D reconstruction. The twist angle is 179.64 degree and the rise is 3.39 angstrom.
Samplealpha-synuclein fiber:
Alpha-synuclein
Function / homologyAmyloid fiber formation / Synuclein / Synuclein / Alpha-synuclein / regulation of phospholipase activity / regulation of acyl-CoA biosynthetic process / neutral lipid metabolic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of mitochondrial electron transport, NADH to ubiquinone / response to desipramine ...Amyloid fiber formation / Synuclein / Synuclein / Alpha-synuclein / regulation of phospholipase activity / regulation of acyl-CoA biosynthetic process / neutral lipid metabolic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of mitochondrial electron transport, NADH to ubiquinone / response to desipramine / negative regulation of monooxygenase activity / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / regulation of glutamate secretion / regulation of reactive oxygen species biosynthetic process / negative regulation of transporter activity / 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 / 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 / negative regulation of histone acetylation / synaptic vesicle transport / negative regulation of microtubule polymerization / dopamine uptake involved in synaptic transmission / nuclear outer membrane / positive regulation of receptor recycling / regulation of dopamine secretion / regulation of macrophage activation / dynein complex binding / negative regulation of dopamine metabolic process / beta-tubulin binding / positive regulation of endocytosis / supramolecular fiber organization / alpha-tubulin binding / phospholipase binding / kinesin binding / response to magnesium ion / response to interferon-gamma / negative regulation of thrombin-activated receptor signaling pathway / cellular response to fibroblast growth factor stimulus / synaptic vesicle endocytosis / cuprous ion binding / regulation of presynapse assembly / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / behavioral response to cocaine / response to interleukin-1 / excitatory postsynaptic potential / inclusion body / regulation of transmembrane transporter activity / Hsp70 protein binding / microglial cell activation / synapse organization / adult locomotory behavior / cellular response to epinephrine stimulus / phospholipid metabolic process / long-term synaptic potentiation / positive regulation of protein serine/threonine kinase activity / fatty acid metabolic process / negative regulation of protein phosphorylation / rough endoplasmic reticulum / receptor internalization / ferrous iron binding / positive regulation of release of sequestered calcium ion into cytosol / synaptic vesicle membrane / protein destabilization / cellular response to copper ion / negative regulation of neuron death / regulation of long-term neuronal synaptic plasticity / tau protein binding / phosphoprotein binding / terminal bouton / positive regulation of inflammatory response / phospholipid binding / mitochondrial intermembrane space / postsynapse / actin cytoskeleton / activation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron death / cell cortex / cellular response to oxidative stress / growth cone / actin binding / mitochondrial inner membrane / histone binding / transcription regulatory region DNA binding / protein N-terminus binding / ribosome / positive regulation of peptidyl-serine phosphorylation
Function and homology information
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 3.07 Å resolution
AuthorsLi YW / Zhao CY / Luo F / Liu Z / Gui X / Luo Z / Zhang X / Li D / Liu C / Li X
CitationJournal: Cell Res. / Year: 2018
Title: Amyloid fibril structure of α-synuclein determined by cryo-electron microscopy.
Authors: Yaowang Li / Chunyu Zhao / Feng Luo / Zhenying Liu / Xinrui Gui / Zhipu Luo / Xiang Zhang / Dan Li / Cong Liu / Xueming Li
Validation ReportPDB-ID: 6a6b

SummaryFull reportAbout validation report
DateDeposition: Jun 27, 2018 / Header (metadata) release: Jul 11, 2018 / Map release: Jul 11, 2018 / Last update: Oct 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6a6b
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6a6b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6988.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.32 Å/pix.
= 264. Å
200 pix
1.32 Å/pix.
= 264. Å
200 pix
1.32 Å/pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.06977273 - 0.14746831
Average (Standard dev.)0.001625986 (0.008289028)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin0.00.00.0
Limit199.0199.0199.0
Spacing200200200
CellA=B=C: 264.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0700.1470.002

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Supplemental data

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Sample components

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Entire alpha-synuclein fiber

EntireName: alpha-synuclein fiber / Number of components: 2

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Component #1: protein, alpha-synuclein fiber

ProteinName: alpha-synuclein fiber / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #2: protein, Alpha-synuclein

ProteinName: Alpha-synuclein / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 6.251097 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 2.393 Å / Delta phi: 179.641 deg.
Sample solutionpH: 7.5
Support film4 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 289 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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