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- EMDB-60234: A self-assembled nanofiber -

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Basic information

Entry
Database: EMDB / ID: EMD-60234
TitleA self-assembled nanofiber
Map data
Sample
  • Complex: A self-assembled nanofiber
    • Protein or peptide: TYR-ALA-TRP-PHE
KeywordsA chemically synthesized peptide that can be self-assembled into nanofiber / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsShi JH / Fang Y / Ma D / Wang HM
Funding support China, 1 items
OrganizationGrant numberCountry
Other government2022YFB3808300 China
CitationJournal: Nat Commun / Year: 2025
Title: Water-regulated viscosity-plasticity phase transitions in a peptide self-assembled muscle-like hydrogel.
Authors: Yu Fang / Junhui Shi / Juan Liang / Dan Ma / Huaimin Wang /
Abstract: The self-assembly of small molecules through non-covalent interactions is an emerging and promising strategy for building dynamic, stable, and large-scale structures. One remaining challenge is ...The self-assembly of small molecules through non-covalent interactions is an emerging and promising strategy for building dynamic, stable, and large-scale structures. One remaining challenge is making the non-covalent interactions occur in the ideal positions to generate strength comparable to that of covalent bonds. This work shows that small molecule YAWF can self-assemble into a liquid-crystal hydrogel (LCH), the mechanical properties of which could be controlled by water. LCH can be used to construct stable solid threads with a length of over 1 meter by applying an external force on 2 µL of gel solution followed by water-regulated crystallization. These solid threads can support 250 times their weight. Cryogenic electron microscopy (Cryo-EM) analysis unravels the three-dimensional structure of the liquid-crystal fiber (elongated helix with C2 symmetry) at an atomic resolution. The multiscale mechanics of this material depend on the specificity of the molecular structure, and the water-controlled hierarchical and sophisticated self-assembly.
History
DepositionMay 21, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60234.png

Downloads & links

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Map

FileDownload / File: emd_60234.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 200 pix.
= 217.4 Å		1.09 Å/pix.
x 200 pix.
= 217.4 Å		1.09 Å/pix.
x 200 pix.
= 217.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.54
Minimum - Maximum-1.4576896 - 2.780164
Average (Standard dev.)0.011521399 (±0.13441752)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 217.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60234_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_60234_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A self-assembled nanofiber

EntireName: A self-assembled nanofiber
Components
  • Complex: A self-assembled nanofiber
    • Protein or peptide: TYR-ALA-TRP-PHE

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Supramolecule #1: A self-assembled nanofiber

SupramoleculeName: A self-assembled nanofiber / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: TYR-ALA-TRP-PHE

MacromoleculeName: TYR-ALA-TRP-PHE / type: protein_or_peptide / ID: 1 / Number of copies: 62 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 585.65 Da
SequenceString:
YAWF

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 5.15 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 811406
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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