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

Basic information

• Entry: Database: EMDB / ID: EMD-6988
• Title: cryo-em structure of alpha-synuclein fiber
• Map data: Density 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.

Sample

• Complex: alpha-synuclein fiber
  • Protein or peptide: Alpha-synuclein

• Keywords: alpha-syn fiber / Parkinson disease / PROTEIN FIBRIL

Function / homology

Function:

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 / synaptic vesicle priming / mitochondrial ATP synthesis coupled electron transport / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / 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

Domain/homology:

Synuclein / Alpha-synuclein / Synuclein

Component:

Alpha-synuclein

• Biological species: Homo sapiens (human)
• Method: helical reconstruction / cryo EM / Resolution: 3.07 Å
• Authors: Li YW / Zhao CY
• Citation: Journal: 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 / ; Abstract: α-Synuclein (α-syn) amyloid fibrils are the major component of Lewy bodies, which are the pathological hallmark of Parkinson's disease (PD) and other synucleinopathies. High-resolution structure of α-syn fibril is important for understanding its assembly and pathological mechanism. Here, we determined a fibril structure of full-length α-syn (1-140) at the resolution of 3.07 Å by cryo-electron microscopy (cryo-EM). The fibrils are cytotoxic, and transmissible to induce endogenous α-syn aggregation in primary neurons. Based on the reconstructed cryo-EM density map, we were able to unambiguously build the fibril structure comprising residues 37-99. The α-syn amyloid fibril structure shows two protofilaments intertwining along an approximate 2 screw axis into a left-handed helix. Each protofilament features a Greek key-like topology. Remarkably, five out of the six early-onset PD familial mutations are located at the dimer interface of the fibril (H50Q, G51D, and A53T/E) or involved in the stabilization of the protofilament (E46K). Furthermore, these PD mutations lead to the formation of fibrils with polymorphic structures distinct from that of the wild-type. Our study provides molecular insight into the fibrillar assembly of α-syn at the atomic level and sheds light on the molecular pathogenesis caused by familial PD mutations of α-syn.

History

Deposition	Jun 27, 2018	-
Header (metadata) release	Jul 11, 2018	-
Map release	Jul 11, 2018	-
Update	Mar 27, 2024	-
Current status	Mar 27, 2024	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_6988.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Density 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.
• Voxel size: X=Y=Z: 1.32 Å

Density

Contour Level	By AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum	-0.06977273 - 0.14746831
Average (Standard dev.)	0.001625986 (±0.008289028)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 200 200 200 Spacing 200 200 200
Cell	A=B=C: 264.0 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.32	1.32	1.32
M x/y/z	200	200	200
origin x/y/z	0.000	0.000	0.000
length x/y/z	264.000	264.000	264.000
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	200	200	200
D min/max/mean	-0.070	0.147	0.002

Supplemental data

Additional map: 3D reconstruction map without applying helical symmetry.

• File: emd_6988_additional.map
• Annotation: 3D reconstruction map without applying helical symmetry.

Half map: 3D reconstruction map using half dataset

• File: emd_6988_half_map_1.map
• Annotation: 3D reconstruction map using half dataset

Half map: 3D reconstruction map using half dataset

• File: emd_6988_half_map_2.map
• Annotation: 3D reconstruction map using half dataset

Sample components

Entire : alpha-synuclein fiber

• Entire: Name: alpha-synuclein fiber

Components

• Complex: alpha-synuclein fiber
  • Protein or peptide: Alpha-synuclein

Supramolecule #1: alpha-synuclein fiber

• Supramolecule: Name: alpha-synuclein fiber / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: Alpha-synuclein

• Macromolecule: Name: Alpha-synuclein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 6.251097 KDa
• Recombinant expression: Organism: Escherichia coli K-12 (bacteria)

Sequence

String:

VLYVGSKTKE GVVHGVATVA EKTKEQVTNV GGAVVTGVTA VAQKTVEGAG SIAAATGFVK KDQ

UniProtKB: Alpha-synuclein

Experimental details

Structure determination

• Method: cryo EM
• Processing: helical reconstruction
• Aggregation state: filament

Sample preparation

• Buffer: pH: 7.5
• Grid: Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE; Details: 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
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Final reconstruction: Applied symmetry - Helical parameters - Δz: 2.393 Å; Applied symmetry - Helical parameters - Δ&Phi: 179.641 °; Applied symmetry - Helical parameters - Axial symmetry: C₁ (asymmetric); Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 43677
• Startup model: Type of model: OTHER / Details: a feature less cylinder
• Final angle assignment: Type: NOT APPLICABLE