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- EMDB-56938: DIT3 nanofibril -

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Basic information

Entry
Database: EMDB / ID: EMD-56938
TitleDIT3 nanofibril
Map datasharpened full map, C6-symmetry
Sample
  • Complex: nanofibril (KVRVSQINM)
    • Protein or peptide: nanofibril peptide (KVRVSQINM)
Keywordsnanofibrils / synthetic peptide / peptide origami / STRUCTURAL PROTEIN
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 1.78 Å
AuthorsStoyanov N / Schmidt M / Faendrich M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1279/Z03 and A03 Germany
CitationJournal: Nature / Year: 2026
Title: Sequence-encoded hexagonal lattices in multichannel peptide nanofibrils.
Authors: Jasmina Gačanin / Francesca Mazzotta / Luis Andre Baptista / Nikolay Stoyanov / Matthias Schmidt / Nico Alleva / Thunchanok Thummaraj / Fanny Bonnicel / Cong Zhou / Lei Gao / Jan Münch / ...Authors: Jasmina Gačanin / Francesca Mazzotta / Luis Andre Baptista / Nikolay Stoyanov / Matthias Schmidt / Nico Alleva / Thunchanok Thummaraj / Fanny Bonnicel / Cong Zhou / Lei Gao / Jan Münch / Mischa Bonn / Marcus Fändrich / Ingo Lieberwirth / Robinson Cortes-Huerto / Katharina Landfester / Tanja Weil /
Abstract: Structural complexity in biological matter arises from molecular information that encodes supramolecular assembly across length scales. Here we show that minimal nine-residue peptides can encode ...Structural complexity in biological matter arises from molecular information that encodes supramolecular assembly across length scales. Here we show that minimal nine-residue peptides can encode discrete lateral interaction motifs that direct supramolecular organization. These motifs generate hexagonal pores and hierarchically tile into multichannel nanofibrils with defined topology. Sequence-encoded amphiphilicity combines a cross-β-dimer, an inversion point and a trimeric junction to create complementary interfaces that couple lateral growth to axial stacking, yielding honeycomb lattices with continuous approximately 5-nm solvent-accessible nanochannels. Cryo-electron microscopy resolves the supramolecular architecture and shows that lattice symmetry and pore geometry are preserved across variants. Systematic perturbations establish sequence-structure rules linking residue position to supramolecular symmetry, lattice propagation and channel topology. Molecular dynamics simulations and vibrational spectroscopy show that the channels remain water accessible and show sequence-tunable hydration. These findings establish that a minimal, sequence-encoded interaction hierarchy can programme long-range supramolecular order, providing a general framework for how short peptides can encode complex, symmetry-defined architectures.
History
DepositionFeb 26, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56938.png

Downloads & links

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Map

FileDownload / File: emd_56938.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened full map, C6-symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 500 pix.
= 365.5 Å		0.73 Å/pix.
x 500 pix.
= 365.5 Å		0.73 Å/pix.
x 500 pix.
= 365.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.731 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.37888923 - 0.75255895
Average (Standard dev.)0.0029679534 (±0.03514093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 365.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56938_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_56938_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_56938_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : nanofibril (KVRVSQINM)

EntireName: nanofibril (KVRVSQINM)
Components
  • Complex: nanofibril (KVRVSQINM)
    • Protein or peptide: nanofibril peptide (KVRVSQINM)

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Supramolecule #1: nanofibril (KVRVSQINM)

SupramoleculeName: nanofibril (KVRVSQINM) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: nanofibril with sequence KVRVSQINM
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: nanofibril peptide (KVRVSQINM)

MacromoleculeName: nanofibril peptide (KVRVSQINM) / type: protein_or_peptide / ID: 1
Details: 3 layers of the asymmetrical unit of the C6 symmetrical nanofibril (KVRVSQINM)
Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.076313 KDa
SequenceString:
KVRVSQINM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4 / Details: phosphate-buffered saline (PBS) and DMSO
GridModel: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 11885 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.791 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.6115 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 1.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.71) / Details: FSC estimation in RELION / Number images used: 171312
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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