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- PDB-28xh: DIT2 nanofibril -

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Basic information

Entry
Database: PDB / ID: 28xh
TitleDIT2 nanofibril
Componentsnanofibril peptide (RVKVSQINM)
KeywordsSTRUCTURAL PROTEIN / nanofibrils / synthetic peptide / peptide origami
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 1.91 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 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Oct 7, 2026Data 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
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nanofibril peptide (RVKVSQINM)
A1: nanofibril peptide (RVKVSQINM)
A2: nanofibril peptide (RVKVSQINM)
AA: nanofibril peptide (RVKVSQINM)
AA1: nanofibril peptide (RVKVSQINM)
AA2: nanofibril peptide (RVKVSQINM)
AB: nanofibril peptide (RVKVSQINM)
AB1: nanofibril peptide (RVKVSQINM)
AB2: nanofibril peptide (RVKVSQINM)
AC: nanofibril peptide (RVKVSQINM)
AC1: nanofibril peptide (RVKVSQINM)
AC2: nanofibril peptide (RVKVSQINM)
AD: nanofibril peptide (RVKVSQINM)
AD1: nanofibril peptide (RVKVSQINM)
AD2: nanofibril peptide (RVKVSQINM)
AE: nanofibril peptide (RVKVSQINM)
AE1: nanofibril peptide (RVKVSQINM)
AE2: nanofibril peptide (RVKVSQINM)
AG: nanofibril peptide (RVKVSQINM)
AG1: nanofibril peptide (RVKVSQINM)
AG2: nanofibril peptide (RVKVSQINM)
B: nanofibril peptide (RVKVSQINM)
B1: nanofibril peptide (RVKVSQINM)
B2: nanofibril peptide (RVKVSQINM)
C: nanofibril peptide (RVKVSQINM)
C1: nanofibril peptide (RVKVSQINM)
C2: nanofibril peptide (RVKVSQINM)
D: nanofibril peptide (RVKVSQINM)
D1: nanofibril peptide (RVKVSQINM)
D2: nanofibril peptide (RVKVSQINM)
E: nanofibril peptide (RVKVSQINM)
E1: nanofibril peptide (RVKVSQINM)
E2: nanofibril peptide (RVKVSQINM)
F: nanofibril peptide (RVKVSQINM)
F1: nanofibril peptide (RVKVSQINM)
F2: nanofibril peptide (RVKVSQINM)
G: nanofibril peptide (RVKVSQINM)
G1: nanofibril peptide (RVKVSQINM)
G2: nanofibril peptide (RVKVSQINM)
H: nanofibril peptide (RVKVSQINM)
H1: nanofibril peptide (RVKVSQINM)
H2: nanofibril peptide (RVKVSQINM)
I: nanofibril peptide (RVKVSQINM)
I1: nanofibril peptide (RVKVSQINM)
I2: nanofibril peptide (RVKVSQINM)
K: nanofibril peptide (RVKVSQINM)
K1: nanofibril peptide (RVKVSQINM)
K2: nanofibril peptide (RVKVSQINM)
L: nanofibril peptide (RVKVSQINM)
L1: nanofibril peptide (RVKVSQINM)
L3: nanofibril peptide (RVKVSQINM)
M: nanofibril peptide (RVKVSQINM)
M1: nanofibril peptide (RVKVSQINM)
M2: nanofibril peptide (RVKVSQINM)
N: nanofibril peptide (RVKVSQINM)
N1: nanofibril peptide (RVKVSQINM)
N2: nanofibril peptide (RVKVSQINM)
O: nanofibril peptide (RVKVSQINM)
O1: nanofibril peptide (RVKVSQINM)
O2: nanofibril peptide (RVKVSQINM)
P: nanofibril peptide (RVKVSQINM)
P1: nanofibril peptide (RVKVSQINM)
P2: nanofibril peptide (RVKVSQINM)
Q: nanofibril peptide (RVKVSQINM)
Q1: nanofibril peptide (RVKVSQINM)
Q2: nanofibril peptide (RVKVSQINM)
R: nanofibril peptide (RVKVSQINM)
R1: nanofibril peptide (RVKVSQINM)
R2: nanofibril peptide (RVKVSQINM)
S: nanofibril peptide (RVKVSQINM)
S1: nanofibril peptide (RVKVSQINM)
S2: nanofibril peptide (RVKVSQINM)
T: nanofibril peptide (RVKVSQINM)
T1: nanofibril peptide (RVKVSQINM)
T2: nanofibril peptide (RVKVSQINM)
U: nanofibril peptide (RVKVSQINM)
U1: nanofibril peptide (RVKVSQINM)
U2: nanofibril peptide (RVKVSQINM)
V: nanofibril peptide (RVKVSQINM)
V1: nanofibril peptide (RVKVSQINM)
V2: nanofibril peptide (RVKVSQINM)
W: nanofibril peptide (RVKVSQINM)
W1: nanofibril peptide (RVKVSQINM)
W2: nanofibril peptide (RVKVSQINM)
X: nanofibril peptide (RVKVSQINM)
X1: nanofibril peptide (RVKVSQINM)
X2: nanofibril peptide (RVKVSQINM)
Y: nanofibril peptide (RVKVSQINM)
Y1: nanofibril peptide (RVKVSQINM)
Y2: nanofibril peptide (RVKVSQINM)
Z: nanofibril peptide (RVKVSQINM)
Z1: nanofibril peptide (RVKVSQINM)
Z2: nanofibril peptide (RVKVSQINM)
AF: nanofibril peptide (RVKVSQINM)
AH: nanofibril peptide (RVKVSQINM)
AI: nanofibril peptide (RVKVSQINM)


Theoretical massNumber of molelcules
Total (without water)103,32696
Polymers103,32696
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 (RVKVSQINM)


Mass: 1076.313 Da / Num. of mol.: 96 / Source method: obtained synthetically
Details: 3 layers of the asymmetrical unit of the C3 symmetrical nanofibril (RVKVSQINM)
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 (RVKVSQINM) / Type: COMPLEX / Details: nanofibril with sequence RVKVSQINM / 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
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: 3534

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2SerialEMimage acquisition
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.409 ° / Axial rise/subunit: 4.781 Å / Axial symmetry: C3
3D reconstructionResolution: 1.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38411 / Symmetry type: HELICAL

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