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- EMDB-46501: Nanotube of F5 -

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Basic information

Entry
Database: EMDB / ID: EMD-46501
TitleNanotube of F5
Map data
Sample
  • Complex: self-assembly of F5 nanotubes
    • Protein or peptide: Nanotube of F5
Keywordsfilament / self-assembly peptide filament / Cryo-EM / peptide fibril / nanotube / bolaphile / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDas A
Funding support United States, 8 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)G20-RR31199 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)SIG S10-RR025067 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U24-GM116790 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)UL1TR000454 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)S10 RR025679 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)GM138756 United States
National Science Foundation (NSF, United States)DBI-1726544 United States
CitationJournal: To Be Published
Title: Surfactant-like peptide-based materials display structural complexity comparable to amyloid fibrils
Authors: Das A / Conticello V / Wang F / Gnewou O / Xuo Z
History
DepositionAug 8, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46501.png

Downloads & links

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Map

FileDownload / File: emd_46501.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.0047457297 - 1.1947699
Average (Standard dev.)0.003497707 (±0.03739158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46501_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_46501_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 : self-assembly of F5 nanotubes

EntireName: self-assembly of F5 nanotubes
Components
  • Complex: self-assembly of F5 nanotubes
    • Protein or peptide: Nanotube of F5

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Supramolecule #1: self-assembly of F5 nanotubes

SupramoleculeName: self-assembly of F5 nanotubes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Nanotube of F5

MacromoleculeName: Nanotube of F5 / type: protein_or_peptide / ID: 1 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 787.068 Da
SequenceString:
(ACE)KIIIFK(NH2)

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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: 4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.27 µm / Nominal defocus min: 0.523 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.24 Å
Applied symmetry - Helical parameters - Δ&Phi: 89.59 °
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: 122105
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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