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- PDB-28xg: DIT3 nanofibril -

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Basic information

Entry
Database: PDB / ID: 28xg
TitleDIT3 nanofibril
Componentsnanofibril peptide (KVRVSQINM)
KeywordsSTRUCTURAL PROTEIN / nanofibrils / synthetic peptide / peptide origami
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 1.78 Å
AuthorsStoyanov, N. / Schmidt, M. / Faendrich, M.
Funding support Germany, 1items
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, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G2: nanofibril peptide (KVRVSQINM)
E2: nanofibril peptide (KVRVSQINM)
F2: nanofibril peptide (KVRVSQINM)
G1: nanofibril peptide (KVRVSQINM)
E1: nanofibril peptide (KVRVSQINM)
F1: nanofibril peptide (KVRVSQINM)
G: nanofibril peptide (KVRVSQINM)
E: nanofibril peptide (KVRVSQINM)
F: nanofibril peptide (KVRVSQINM)
I2: nanofibril peptide (KVRVSQINM)
K2: nanofibril peptide (KVRVSQINM)
I1: nanofibril peptide (KVRVSQINM)
K1: nanofibril peptide (KVRVSQINM)
I: nanofibril peptide (KVRVSQINM)
K: nanofibril peptide (KVRVSQINM)
D2: nanofibril peptide (KVRVSQINM)
B2: nanofibril peptide (KVRVSQINM)
C2: nanofibril peptide (KVRVSQINM)
H2: nanofibril peptide (KVRVSQINM)
A2: nanofibril peptide (KVRVSQINM)
D1: nanofibril peptide (KVRVSQINM)
B1: nanofibril peptide (KVRVSQINM)
C1: nanofibril peptide (KVRVSQINM)
H1: nanofibril peptide (KVRVSQINM)
A1: nanofibril peptide (KVRVSQINM)
D: nanofibril peptide (KVRVSQINM)
B: nanofibril peptide (KVRVSQINM)
C: nanofibril peptide (KVRVSQINM)
H: nanofibril peptide (KVRVSQINM)
A: nanofibril peptide (KVRVSQINM)


Theoretical massNumber of molelcules
Total (without water)32,28930
Polymers32,28930
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide ...
nanofibril peptide (KVRVSQINM)


Mass: 1076.313 Da / Num. of mol.: 30 / Source method: obtained synthetically
Details: 3 layers of the asymmetrical unit of the C6 symmetrical nanofibril (KVRVSQINM)
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: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: nanofibril (KVRVSQINM) / Type: COMPLEX / Details: nanofibril with sequence KVRVSQINM / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.4 / Details: phosphate-buffered saline (PBS) and DMSO
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS 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: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 11885

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.71particle selection
2SerialEMimage acquisition
13cryoSPARC4.713D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.6115 ° / Axial rise/subunit: 4.791 Å / Axial symmetry: C6
3D reconstructionResolution: 1.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171312 / Details: FSC estimation in RELION / Symmetry type: HELICAL

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