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- EMDB-47736: CNS-11g alone fibril -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47736
TitleCNS-11g alone fibril
Map data
Sample
  • Complex: CNS-11g alone fibril
KeywordsSmall molecule fibril assembly / Amyloid disaggregator. / UNKNOWN FUNCTION
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLu J / Sawaya MR
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_47736.png

Downloads & links

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Map

FileDownload / File: emd_47736.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
1.06 Å/pix.
x 288 pix.
= 304.704 Å		1.06 Å/pix.
x 288 pix.
= 304.704 Å		1.06 Å/pix.
x 288 pix.
= 304.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.003
Minimum - Maximum-16.659331999999999 - 23.784389999999998
Average (Standard dev.)0.00000000024208 (±0.9942931)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 304.70398 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47736_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47736_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 : CNS-11g alone fibril

EntireName: CNS-11g alone fibril
Components
  • Complex: CNS-11g alone fibril

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Supramolecule #1: CNS-11g alone fibril

SupramoleculeName: CNS-11g alone fibril / type: complex / ID: 1 / Parent: 0 / Details: A fibrillar assembly of small molecules CNS-11g
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 397.5 MDa

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 319 K / Instrument: FEI VITROBOT MARK IV
DetailsCNS-11g alone fibrils

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 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: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 2.18 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11592
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Gaussian blob
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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