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- EMDB-48237: Cryo-EM of helical fibers formed by (NAP)FFGPQYQP -

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Basic information

Entry
Database: EMDB / ID: EMD-48237
TitleCryo-EM of helical fibers formed by (NAP)FFGPQYQP
Map datafull map
Sample
  • Complex: (I7L)FFGPQYQP
    • Protein or peptide: (I7L)FFGPQYQP
Keywordspeptide fiber / helical polymer / protein fibril
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsZia A / Qiao Y / Xu B / Wang F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA142746 United States
CitationJournal: Angew Chem Int Ed Engl / Year: 2025
Title: Intrinsically Disordered Peptide Nanofibers from a Structured Motif Within Proteins.
Authors: Yuchen Qiao / Ayisha Zia / Adrianna Shy / Grace Wu / Matthew Chu / Zhiyu Liu / Fengbin Wang / Bing Xu /
Abstract: Intrinsically disordered regions (IDRs) are ubiquitous in proteins, orchestrating complex cellular signaling through higher-order protein assemblies. However, the properties and functions of ...Intrinsically disordered regions (IDRs) are ubiquitous in proteins, orchestrating complex cellular signaling through higher-order protein assemblies. However, the properties and functions of intrinsically disordered peptide (IDP) assemblies are largely underexplored. This work unveiled a facile strategy for engineering IDP assemblies. We demonstrate that conjugating a structured motif derived from a protein's phosphorylation site to a self-assembling tripeptide unexpectedly yields self-assembled nanofibers with intrinsic disorder. Specifically, by using a glycine linker to attach a pentapeptide derived from a phosphorylation site within a random coil region of SRC kinase to the C-terminus of a widely used self-assembling enabler, we generated a phosphorylated octapeptide. The octapeptide exhibits cell compatibility and forms a hydrogel upon dephosphorylation of the phosphooctapeptide. Cryo-electron microscopy (cryo-EM) structural analysis of the nanofibers reveals that the peptides adopt two types of helical arrangements but exhibit intrinsic disorder at the periphery of the nanofibers. The hydrogels exhibit decreased protein adsorption with increasing peptide concentration. This study represents the first instance of a structured random coil within a protein transitioning into an intrinsically disordered state within self-assembled peptide nanofibers, expanding the pool of peptide sequences for IDPs and providing valuable insights for the engineering of peptide nanofibers with intrinsic disorder for the development of cell-compatible biomaterials.
History
DepositionDec 10, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48237.png

Downloads & links

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Map

FileDownload / File: emd_48237.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: 0.253
Minimum - Maximum-0.031204654 - 1.4366322
Average (Standard dev.)0.003605422 (±0.036419477)
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 A

Fileemd_48237_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_48237_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : (I7L)FFGPQYQP

EntireName: (I7L)FFGPQYQP
Components
  • Complex: (I7L)FFGPQYQP
    • Protein or peptide: (I7L)FFGPQYQP

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Supramolecule #1: (I7L)FFGPQYQP

SupramoleculeName: (I7L)FFGPQYQP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: (I7L)FFGPQYQP

MacromoleculeName: (I7L)FFGPQYQP / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.151267 KDa
SequenceString:
(I7L)FFGPQYQP

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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: 5.04 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.55 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 858964
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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