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- EMDB-58514: Helical reconstruction of FQ(Pyr) filaments -

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Basic information

Entry
Database: EMDB / ID: EMD-58514
TitleHelical reconstruction of FQ(Pyr) filaments
Map dataSharpened map
Sample
  • Complex: Self-assembling filaments of the non-natural dipeptide FQ(Pyr)
    • Other: FQ(Pyr)
KeywordsSynthetic Peptide / Filament / UNKNOWN FUNCTION
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 1.65 Å
AuthorsNeuhaus A / Broutzakis G / Gatsogiannis C
Funding support Germany, Japan, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)496113311 Germany
Japan Society for the Promotion of Science (JSPS)25H00429 Japan
Japan Society for the Promotion of Science (JSPS)22K21346 Japan
Japan Science and Technology251044983 Japan
CitationJournal: Nat Commun / Year: 2026
Title: Atomic-precision π-driven peptide hydrogel nanofibers with ordered water channels.
Authors: Ayaka Ueda / George Broutzakis / Alexander Neuhaus / David Ens / Dominik Mählmann / Lisa Schlichter / Hideya Kono / Akiko Yagi / Kazuma Amaike / Christos Gatsogiannis / Bart Jan Ravoo / Kenichiro Itami /
Abstract: Aromatic interactions organize molecules into ordered supramolecular architectures, while peptides form functional soft materials through hydrogen bonding and water-mediated assembly. In peptide- ...Aromatic interactions organize molecules into ordered supramolecular architectures, while peptides form functional soft materials through hydrogen bonding and water-mediated assembly. In peptide-based systems, strong aromatic stacking is typically achieved by terminal capping, whereas terminally uncapped peptides organize water through polar end groups but rarely form highly ordered materials. Here we show that a π-extended aromatic unit can be integrated into a terminally uncapped peptide to create a class of supramolecular hydrogels with structural order. A pyrene-modified dipeptide hierarchically assembles into monodisperse helical nanofibers and self-healing hydrogels. Cryo-electron microscopy resolves the nanofibers at near-atomic precision (1.7 Å), revealing tightly packed protofilaments, continuous ordered water channels, and a unidirectional dipole extending along the fiber. These results demonstrate how reinforced aromatic stacking, polar interactions, and cooperative water organization can be orchestrated to generate emergent electrostatics and mechanical resilience, bridging conjugated materials and biomolecular matter, enabling functional soft materials inaccessible to either domain alone.
History
DepositionJun 12, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58514.png

Downloads & links

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Map

FileDownload / File: emd_58514.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.45 Å/pix.
x 416 pix.
= 188.864 Å		0.45 Å/pix.
x 416 pix.
= 188.864 Å		0.45 Å/pix.
x 416 pix.
= 188.864 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.454 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.06644497 - 0.16053487
Average (Standard dev.)0.00082846323 (±0.010008865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 188.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_58514_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Locally filtered map

Fileemd_58514_additional_1.map
AnnotationLocally filtered map
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Additional map: Local resolution map

Fileemd_58514_additional_2.map
AnnotationLocal resolution map
Projections & Slices
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Additional map: Unsharpened map

Fileemd_58514_additional_3.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_58514_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_58514_half_map_2.map
AnnotationHalf map A
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Sample components

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Entire : Self-assembling filaments of the non-natural dipeptide FQ(Pyr)

EntireName: Self-assembling filaments of the non-natural dipeptide FQ(Pyr)
Components
  • Complex: Self-assembling filaments of the non-natural dipeptide FQ(Pyr)
    • Other: FQ(Pyr)

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Supramolecule #1: Self-assembling filaments of the non-natural dipeptide FQ(Pyr)

SupramoleculeName: Self-assembling filaments of the non-natural dipeptide FQ(Pyr)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: FQ(Pyr)

MacromoleculeName: FQ(Pyr) / type: other / ID: 1
Details: Non-natural dipeptide, L-phenylalanyl-L-glutamine (FQ) substituted with a pyrene-based pi-extended aromatic unit on the glutamine side chain
Classification: other
Source (natural)Organism: synthetic construct (others)
SequenceString:
FQ

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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
Component:
ConcentrationFormulaName
50.0 mMNaOHsodium hydroxide
10.0 mg/mlGdLglucono-gamma-lactone
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / 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 / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 270000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.358 Å
Applied symmetry - Helical parameters - Δ&Phi: 90.609 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 1.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 263876
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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