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- EMDB-77045: 3,5-difluoro-L-phenylalanine bolaphile peptide -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-77045
Title3,5-difluoro-L-phenylalanine bolaphile peptide
Map data
Sample
  • Complex: Synthetic amyloid
    • Protein or peptide: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2
KeywordsPeptide nanotube / Amphiphile / Amyloids / helical / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDas A / Conticello VP
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Chemical Editing Reveals Atomic-Level Control of Supramolecular Structure in Self-Assembling Peptides
Authors: Das A / Zia A / Eastep GN / Wang F / Conticello VP
History
DepositionMay 4, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77045.png

Downloads & links

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Map

FileDownload / File: emd_77045.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å		0.84 Å/pix.
x 360 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.23
Minimum - Maximum-0.05983433 - 13.111291
Average (Standard dev.)0.121382214 (±0.79773945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_77045_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77045_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Synthetic amyloid

EntireName: Synthetic amyloid
Components
  • Complex: Synthetic amyloid
    • Protein or peptide: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2

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Supramolecule #1: Synthetic amyloid

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

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Macromolecule #1: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2

MacromoleculeName: ACE-LYS-ILE-ILE-ILE-WFP-LYS-NH2 / type: protein_or_peptide / ID: 1 / Number of copies: 64 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 823.049 Da
SequenceString:
(ACE)KIII(WFP)K(NH2)

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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: 3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.45506 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.19 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 7069
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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