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- PDB-8zm0: A self-assembled nanofiber -

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Basic information

Entry
Database: PDB / ID: 8zm0
TitleA self-assembled nanofiber
ComponentsTYR-ALA-TRP-PHE
KeywordsDE NOVO PROTEIN / A chemically synthesized peptide that can be self-assembled into nanofiber
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsShi, J.H. / Fang, Y. / Ma, D. / Wang, H.M.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Dec 24, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 2.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: TYR-ALA-TRP-PHE
b: TYR-ALA-TRP-PHE
d: TYR-ALA-TRP-PHE
f: TYR-ALA-TRP-PHE
g: TYR-ALA-TRP-PHE
s: TYR-ALA-TRP-PHE
B: TYR-ALA-TRP-PHE
N: TYR-ALA-TRP-PHE
h: TYR-ALA-TRP-PHE
n: TYR-ALA-TRP-PHE
t: TYR-ALA-TRP-PHE
z: TYR-ALA-TRP-PHE
C: TYR-ALA-TRP-PHE
I: TYR-ALA-TRP-PHE
O: TYR-ALA-TRP-PHE
i: TYR-ALA-TRP-PHE
o: TYR-ALA-TRP-PHE
u: TYR-ALA-TRP-PHE
0: TYR-ALA-TRP-PHE
D: TYR-ALA-TRP-PHE
J: TYR-ALA-TRP-PHE
P: TYR-ALA-TRP-PHE
j: TYR-ALA-TRP-PHE
p: TYR-ALA-TRP-PHE
v: TYR-ALA-TRP-PHE
1: TYR-ALA-TRP-PHE
k: TYR-ALA-TRP-PHE
S: TYR-ALA-TRP-PHE
T: TYR-ALA-TRP-PHE
V: TYR-ALA-TRP-PHE
Y: TYR-ALA-TRP-PHE
6: TYR-ALA-TRP-PHE
7: TYR-ALA-TRP-PHE
A: TYR-ALA-TRP-PHE
G: TYR-ALA-TRP-PHE
M: TYR-ALA-TRP-PHE
U: TYR-ALA-TRP-PHE
m: TYR-ALA-TRP-PHE
9: TYR-ALA-TRP-PHE
y: TYR-ALA-TRP-PHE
H: TYR-ALA-TRP-PHE
5: TYR-ALA-TRP-PHE
W: TYR-ALA-TRP-PHE
4: TYR-ALA-TRP-PHE
X: TYR-ALA-TRP-PHE
Z: TYR-ALA-TRP-PHE
E: TYR-ALA-TRP-PHE
K: TYR-ALA-TRP-PHE
Q: TYR-ALA-TRP-PHE
c: TYR-ALA-TRP-PHE
8: TYR-ALA-TRP-PHE
q: TYR-ALA-TRP-PHE
w: TYR-ALA-TRP-PHE
2: TYR-ALA-TRP-PHE
F: TYR-ALA-TRP-PHE
L: TYR-ALA-TRP-PHE
R: TYR-ALA-TRP-PHE
e: TYR-ALA-TRP-PHE
l: TYR-ALA-TRP-PHE
r: TYR-ALA-TRP-PHE
x: TYR-ALA-TRP-PHE
3: TYR-ALA-TRP-PHE


Theoretical massNumber of molelcules
Total (without water)36,31062
Polymers36,31062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
TYR-ALA-TRP-PHE


Mass: 585.650 Da / Num. of mol.: 62 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: A self-assembled nanofiber / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmerty
IDImage processing-IDAngular rotation/subunit (°)Axial rise/subunit (Å)Axial symmetry
115.154.6C2
215.154.6C2
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 811406 / Symmetry type: HELICAL

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