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- EMDB-46060: Self assembled nanotube of L5 -

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Basic information

Entry
Database: EMDB / ID: EMD-46060
TitleSelf assembled nanotube of L5
Map data
Sample
  • Complex: self-assembly of L5 nanotubes
    • Protein or peptide: L5 nanotube
Keywordsfilament / self-assembly peptide filament / peptide fibril / nanotube / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsDas A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Faraday Discuss / Year: 2025
Title: Surfactant-like peptide gels are based on cross-β amyloid fibrils.
Authors: Abhinaba Das / Ordy Gnewou / Xiaobing Zuo / Fengbin Wang / Vincent P Conticello /
Abstract: Surfactant-like peptides, in which hydrophilic and hydrophobic residues are encoded within different domains in the peptide sequence, undergo facile self-assembly in aqueous solution to form ...Surfactant-like peptides, in which hydrophilic and hydrophobic residues are encoded within different domains in the peptide sequence, undergo facile self-assembly in aqueous solution to form supramolecular hydrogels. These peptides have been explored extensively as substrates for the creation of functional materials since a wide variety of amphipathic sequences can be prepared from commonly available amino acid precursors. The self-assembly behavior of surfactant-like peptides has been compared to that observed for small molecule amphiphiles in which nanoscale phase separation of the hydrophobic domains drives the self-assembly of supramolecular structures. Here, we investigate the relationship between sequence and supramolecular structure for a pair of bola-amphiphilic peptides, Ac-KLIIIK-NH (L2) and Ac-KIIILK-NH (L5). Despite similar length, composition, and polar sequence pattern, L2 and L5 form morphologically distinct assemblies, nanosheets and nanotubes, respectively. Cryo-EM helical reconstruction was employed to determine the structure of the L5 nanotube at near-atomic resolution. Rather than displaying self-assembly behavior analogous to conventional amphiphiles, the packing arrangement of peptides in the L5 nanotube displayed steric zipper interfaces that resembled those observed in the structures of β-amyloid fibrils. Like amyloids, the supramolecular structures of the L2 and L5 assemblies were sensitive to conservative amino acid substitutions within an otherwise identical amphipathic sequence pattern. This study highlights the need to better understand the relationship between sequence and supramolecular structure to facilitate the development of functional peptide-based materials for biomaterials applications.
History
DepositionAug 3, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46060.png

Downloads & links

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Map

FileDownload / File: emd_46060.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.72
Minimum - Maximum-0.08832582 - 10.070197
Average (Standard dev.)0.09414994 (±0.65518403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_46060_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #2

Fileemd_46060_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : self-assembly of L5 nanotubes

EntireName: self-assembly of L5 nanotubes
Components
  • Complex: self-assembly of L5 nanotubes
    • Protein or peptide: L5 nanotube

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Supramolecule #1: self-assembly of L5 nanotubes

SupramoleculeName: self-assembly of L5 nanotubes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: L5 nanotube

MacromoleculeName: L5 nanotube / type: protein_or_peptide / ID: 1 / Number of copies: 45 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 753.052 Da
SequenceString:
(ACE)KIIILK(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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 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: 4.94 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.77 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 702524
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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