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- EMDB-70201: Cryo-EM of VEVAG Peptide 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-70201
TitleCryo-EM of VEVAG Peptide 1
Map dataFULL MAP
Sample
  • Complex: VEVAG peptide fibril
    • Protein or peptide: pi-conjugated peptide
    • Ligand: 4,4'-(thiophene-2,5-diyl)dibenzoic acid
Keywordspeptide fiber / helical polymer / protein fibril
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRich-New ST / Wang R / Zia A / Tovar JD / Wang F
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70201.png

Downloads & links

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Map

FileDownload / File: emd_70201.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFULL MAP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 320 pix.
= 358.4 Å		1.12 Å/pix.
x 320 pix.
= 358.4 Å		1.12 Å/pix.
x 320 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-0.017618136 - 1.6677799
Average (Standard dev.)0.0017225043 (±0.03033845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HALF MAP B

Fileemd_70201_half_map_1.map
AnnotationHALF MAP B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HALF MAP A

Fileemd_70201_half_map_2.map
AnnotationHALF MAP A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VEVAG peptide fibril

EntireName: VEVAG peptide fibril
Components
  • Complex: VEVAG peptide fibril
    • Protein or peptide: pi-conjugated peptide
    • Ligand: 4,4'-(thiophene-2,5-diyl)dibenzoic acid

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Supramolecule #1: VEVAG peptide fibril

SupramoleculeName: VEVAG peptide fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: pi-conjugated peptide

MacromoleculeName: pi-conjugated peptide / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 473.52 Da
SequenceString:
GAVEV

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Macromolecule #2: 4,4'-(thiophene-2,5-diyl)dibenzoic acid

MacromoleculeName: 4,4'-(thiophene-2,5-diyl)dibenzoic acid / type: ligand / ID: 2 / Number of copies: 3 / Formula: A1B9Y
Molecular weightTheoretical: 324.35 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.75 Å
Applied symmetry - Helical parameters - Δ&Phi: -4.29 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 304634
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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