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- EMDB-47732: Complex fibril structure of MSA alpha-synuclein with CNS-11g at 4... -

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Basic information

Entry
Database: EMDB / ID: EMD-47732
TitleComplex fibril structure of MSA alpha-synuclein with CNS-11g at 4 hours
Map data
Sample
  • Organelle or cellular component: Alpha-synuclein with CNS-11g
    • Protein or peptide: Alpha-synuclein
  • Ligand: 2-(4-benzyl-1-oxophthalazin-2(1H)-yl)-N-(2,6-dimethylphenyl)acetamide
KeywordsComplex structure of alpha-synuclein type I with small molecule CNS-11g incubated for 4 hours. / STRUCTURAL PROTEIN
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 / 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 / dopamine biosynthetic process / response to iron(II) ion / positive regulation of neurotransmitter secretion / SNARE complex assembly / negative regulation of dopamine metabolic process / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / regulation of norepinephrine uptake / negative regulation of microtubule polymerization / regulation of locomotion / synaptic vesicle transport / 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 / dynein complex binding / positive regulation of receptor recycling / 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 / regulation of presynapse assembly / response to type II interferon / negative regulation of serotonin uptake / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / supramolecular fiber organization / phospholipid metabolic process / cellular response to fibroblast growth factor stimulus / inclusion body / axon terminus / 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 / growth cone / actin binding / 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 / mitochondrial outer membrane / oxidoreductase activity
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLu J / Sawaya MR / Ge P / Boyer DR / Eisenberg DS
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1R01 AG07895 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1 AG065407 United States
CitationJournal: To Be Published
Title: The small molecule CNS-11g forms amyloid-like fibrils that disassemble pathological alpha-synuclein fibrils
Authors: Lu J / Sawaya MR / Cheng XY / Murrali MG / Ge P / Jiang YX / Cascio D / Lutter L / Boyer DR / Williams CK / Shino M / Feigon J / Chaturvedi S / Alexandrova A / Eisenberg DS
History
DepositionNov 6, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47732.png

Downloads & links

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Map

FileDownload / File: emd_47732.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.923
Minimum - Maximum-11.739884 - 18.517488
Average (Standard dev.)-0.000000000003616 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 300.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47732_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_47732_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Alpha-synuclein with CNS-11g

EntireName: Alpha-synuclein with CNS-11g
Components
  • Organelle or cellular component: Alpha-synuclein with CNS-11g
    • Protein or peptide: Alpha-synuclein
  • Ligand: 2-(4-benzyl-1-oxophthalazin-2(1H)-yl)-N-(2,6-dimethylphenyl)acetamide

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Supramolecule #1: Alpha-synuclein with CNS-11g

SupramoleculeName: Alpha-synuclein with CNS-11g / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: The complex structure of alpha-synuclein fibrils extracted from Multiple System Atrophy patient brain, incubated with CNS-11g at 37C for 4 hours
Source (natural)Organism: Homo sapiens (human) / Organ: brain / Tissue: Cerebellum
Molecular weightTheoretical: 14.5 kDa/nm

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Macromolecule #1: Alpha-synuclein

MacromoleculeName: Alpha-synuclein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.476108 KDa
SequenceString:
MDVFMKGLSK AKEGVVAAAE KTKQGVAEAA GKTKEGVLYV GSKTKEGVVH GVATVAEKTK EQVTNVGGAV VTGVTAVAQK TVEGAGSIA AATGFVKKDQ LGKNEEGAPQ EGILEDMPVD PDNEAYEMPS EEGYQDYEPE A

UniProtKB: Alpha-synuclein

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Macromolecule #2: 2-(4-benzyl-1-oxophthalazin-2(1H)-yl)-N-(2,6-dimethylphenyl)acetamide

MacromoleculeName: 2-(4-benzyl-1-oxophthalazin-2(1H)-yl)-N-(2,6-dimethylphenyl)acetamide
type: ligand / ID: 2 / Number of copies: 5 / Formula: A1BGB
Molecular weightTheoretical: 397.469 Da

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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: 7.4 / Details: 30mM Tris-HCl, pH 7.4, with 1% DMSO
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 319 K / Instrument: FEI VITROBOT MARK IV
DetailsThe complex structure of alpha-synuclein fibrils extracted from Multiple System Atrophy patient brain, incubated with CNS-11g at 37C for 4 hours

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 130000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 1.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.79 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.427 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19408
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xyo

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

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