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- PDB-9h7u: Hexagonally Ordered Nanofibrils Easily Yield by dual Amphiphilic ... -

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Basic information

Entry
Database: PDB / ID: 9h7u
TitleHexagonally Ordered Nanofibrils Easily Yield by dual Amphiphilic Self-Assembling Peptide
ComponentsPeptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
KeywordsPROTEIN FIBRIL / synthetic peptide / peptide nanofibril / amyloid / HONEY ASAP
Biological speciesother sequences (unknown)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsMazzotta, F. / Baptista, L.A. / Schmidt, M. / Gacanin, J. / Lieberwirth, I. / Weil, T. / Landfester, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission860914European Union
CitationJournal: To Be Published
Title: Hexagonally Ordered Nanofibrils Easily Yield by dual Amphiphilic Self-Assembling Peptide: HONEY ASAP
Authors: Mazzotta, F. / Baptista, L.A. / Schmidt, M. / Lieberwirth, I. / Landfester, K.
History
DepositionOct 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Aa: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ab: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ac: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ad: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ae: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Af: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ag: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ah: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ai: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Aj: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ak: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Al: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Am: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
An: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ao: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ap: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Aq: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ar: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ci: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cj: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ck: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cl: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cm: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cn: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Co: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cp: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cq: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cr: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cs: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ct: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cu: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cv: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cw: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cx: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cy: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Cz: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Eq: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Er: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Es: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Et: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Eu: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ev: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ew: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ex: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ey: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ez: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Fa: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Fb: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Fc: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Fd: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Fe: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Ff: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Fg: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET
Fh: Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET


Theoretical massNumber of molelcules
Total (without water)56,60854
Polymers56,60854
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 ...
Peptide LYS-VAL-LYS-VAL-SER-GLN-ILE-ASN-MET


Mass: 1048.299 Da / Num. of mol.: 54 / Source method: obtained synthetically / Source: (synth.) other sequences (unknown)
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: Nanofibrils from dual amphiphilic synthetic peptide / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: other sequences (unknown)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39.28839 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4MotionCorr2CTF correction
7Cootmodel fitting
12RELION43D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: -0.64 ° / Axial rise/subunit: 4.77 Å / Axial symmetry: C6
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108623 / Symmetry type: HELICAL

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