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- EMDB-62257: Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B -

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Basic information

Entry
Database: EMDB / ID: EMD-62257
TitleCryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B
Map data
Sample
  • Complex: Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B
    • Protein or peptide: Alpha-synuclein
    • Protein or peptide: Alpha-synuclein
  • Ligand: (2~{R})-1-fluoranyl-3-[[2-[(~{E})-2-[5-[6-(methylamino)pyridin-3-yl]pyridin-2-yl]ethenyl]-1,3-benzothiazol-6-yl]oxy]propan-2-ol
  • Ligand: water
Keywordsamyloid fibril / complex / PROTEIN FIBRIL
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 / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber ...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 / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / regulation of synaptic vesicle recycling / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / dopamine biosynthetic process / response to iron(II) ion / SNARE complex assembly / negative regulation of dopamine metabolic process / positive regulation of neurotransmitter secretion / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / regulation of norepinephrine uptake / regulation of locomotion / synaptic vesicle transport / negative regulation of microtubule polymerization / transporter regulator activity / synaptic vesicle priming / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / mitochondrial ATP synthesis coupled electron transport / positive regulation of receptor recycling / dynein complex binding / cuprous ion binding / nuclear outer membrane / response to magnesium ion / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / synaptic vesicle endocytosis / enzyme inhibitor activity / cysteine-type endopeptidase inhibitor activity / response to type II interferon / negative regulation of serotonin uptake / regulation of presynapse assembly / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / supramolecular fiber organization / cellular response to fibroblast growth factor stimulus / phospholipid metabolic process / axon terminus / inclusion body / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / cellular response to copper ion / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / adult locomotory behavior / excitatory postsynaptic potential / protein tetramerization / phosphoprotein binding / microglial cell activation / ferrous iron binding / fatty acid metabolic process / regulation of long-term neuronal synaptic plasticity / synapse organization / PKR-mediated signaling / protein destabilization / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / terminal bouton / positive regulation of inflammatory response / synaptic vesicle membrane / actin cytoskeleton / actin binding / growth cone / cellular response to oxidative stress / neuron apoptotic process / cell cortex / histone binding / response to lipopolysaccharide / microtubule binding / chemical synaptic transmission / amyloid fibril formation / molecular adaptor activity / negative regulation of neuron apoptotic process / oxidoreductase activity / mitochondrial outer membrane
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhang SQ / Li D / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B
Authors: Zhang SQ / Liu C
History
DepositionNov 1, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62257.png

Downloads & links

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Map

FileDownload / File: emd_62257.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.06655287 - 0.08970487
Average (Standard dev.)0.0003222555 (±0.0031720991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62257_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62257_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B

EntireName: Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B
Components
  • Complex: Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B
    • Protein or peptide: Alpha-synuclein
    • Protein or peptide: Alpha-synuclein
  • Ligand: (2~{R})-1-fluoranyl-3-[[2-[(~{E})-2-[5-[6-(methylamino)pyridin-3-yl]pyridin-2-yl]ethenyl]-1,3-benzothiazol-6-yl]oxy]propan-2-ol
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B

SupramoleculeName: Cryo-EM structure of FD4-bound alpha-synuclein fibril polymorph 6A6B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Alpha-synuclein

MacromoleculeName: Alpha-synuclein / type: protein_or_peptide / ID: 1
Details: The sequence (UNK)(UNK)(UNK)(UNK)(UNK) (molecule 1) represents a segment of the N-terminal amino acids (1-36) of alpha-synuclein. However, due to insufficient EM density to observe the amino ...Details: The sequence (UNK)(UNK)(UNK)(UNK)(UNK) (molecule 1) represents a segment of the N-terminal amino acids (1-36) of alpha-synuclein. However, due to insufficient EM density to observe the amino acid side chains, it is unclear which specific segment of alpha-synuclein is visualized in the structure. Therefore, we opted to modeled it as poly-UNK.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 443.539 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #2: Alpha-synuclein

MacromoleculeName: Alpha-synuclein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.820836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VLYVGSKTKE GVVHGVATVA EKTKEQVTNV GGAVVTGVTA VAQKTVEGAG SIAAATGFVK KDQLGKNEEG APQEGILEDM PVDPDNEAY EMPSEEGYQD YEPEA

UniProtKB: Alpha-synuclein

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Macromolecule #3: (2~{R})-1-fluoranyl-3-[[2-[(~{E})-2-[5-[6-(methylamino)pyridin-3-...

MacromoleculeName: (2~{R})-1-fluoranyl-3-[[2-[(~{E})-2-[5-[6-(methylamino)pyridin-3-yl]pyridin-2-yl]ethenyl]-1,3-benzothiazol-6-yl]oxy]propan-2-ol
type: ligand / ID: 3 / Number of copies: 12 / Formula: A1EFL
Molecular weightTheoretical: 436.502 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 48 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.41 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.62 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 363619
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6a6b

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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