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- PDB-9o7k: Cryo-EM of pi-conjugated Peptide 2 (9 strands) -

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Basic information

Entry
Database: PDB / ID: 9o7k
TitleCryo-EM of pi-conjugated Peptide 2 (9 strands)
Componentspi-conjugated peptide
KeywordsPROTEIN FIBRIL / peptide fiber / helical polymer
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsRich-New, S.T. / Wang, R. / Zia, A. / Tovar, J.D. / Wang, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
CitationJournal: ACS Macro Lett / Year: 2025
Title: Cryo-EM Visualization of Intermolecular π-Electron Interactions within π-Conjugated Peptidic Supramolecular Polymers.
Authors: Shane T Rich-New / Runlai Wang / Ayisha Zia / Fengbin Wang / John D Tovar /
Abstract: The self-assembly of "π-peptides" - molecules with π-electron cores substituted with two or more oligopeptide chains - brings organic electronic function into biologically relevant nanomaterials. ...The self-assembly of "π-peptides" - molecules with π-electron cores substituted with two or more oligopeptide chains - brings organic electronic function into biologically relevant nanomaterials. π-Peptides assemble into fibrillar nanomaterials as driven by enthalpic peptide-based hydrogen bonding networks and pi-core-based quadrupolar interactions. A large body of spectroscopic, morphological and computational studies informs on the nature of the self-assembly process and the resulting nanostructures, but detailed structural information has remained elusive. Inspired by the recent use of cryogenic electron microscopy (cryo-EM) to provide high-resolution structures for synthetic peptide nanomaterials, we present here the use of cryo-EM to offer ca. 3 Å resolution of π-peptide nanomaterial assemblies, visualizing for the first time the nature of the intermolecular π-core electronic interactions responsible for energy transport through these supramolecular materials.
History
DepositionApr 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pi-conjugated peptide
D: pi-conjugated peptide
B: pi-conjugated peptide
F: pi-conjugated peptide
C: pi-conjugated peptide
H: pi-conjugated peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8989
Polymers2,8416
Non-polymers1,0573
Water00
1
A: pi-conjugated peptide
D: pi-conjugated peptide
B: pi-conjugated peptide
F: pi-conjugated peptide
C: pi-conjugated peptide
H: pi-conjugated peptide
hetero molecules
x 20


Theoretical massNumber of molelcules
Total (without water)77,967180
Polymers56,822120
Non-polymers21,14460
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation19
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 20 / Rise per n subunits: 1.6 Å / Rotation per n subunits: -120.4 °)

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Components

#1: Protein/peptide
pi-conjugated peptide


Mass: 473.520 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-A1B9Z / 2,2'-[thiophene-2,5-diyldi(4,1-phenylene)]diacetic acid


Mass: 352.404 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H16O4S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: VEVAG peptide fibril / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7
SpecimenEmbedding 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: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -120.4 ° / Axial rise/subunit: 1.6 Å / Axial symmetry: C1
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2342281 / Symmetry type: HELICAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0164806
ELECTRON MICROSCOPYf_angle_d1.3996426
ELECTRON MICROSCOPYf_dihedral_angle_d36.2191350
ELECTRON MICROSCOPYf_chiral_restr0.067648
ELECTRON MICROSCOPYf_plane_restr0.005810

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