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- EMDB-25714: Cryo-EM of NBD-ffsy filaments (class 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-25714
TitleCryo-EM of NBD-ffsy filaments (class 1)
Map dataCryo-EM of NBD-ffsy filaments (class 1)
Sample
  • Complex: self-assemble NBD-ffsy nanotube
    • Protein or peptide: NBD-ffsy peptide
Keywordstranscytosis / hydrogel / peptides / nanofibers / spheroids / self-assembly peptide filament / PROTEIN FIBRIL
Biological speciesSynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang F / Guo J
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA142746 United States
National Science Foundation (NSF, United States)DMR-2011846 United States
CitationJournal: Nat Nanotechnol / Year: 2023
Title: Cell spheroid creation by transcytotic intercellular gelation.
Authors: Jiaqi Guo / Fengbin Wang / Yimeng Huang / Hongjian He / Weiyi Tan / Meihui Yi / Edward H Egelman / Bing Xu /
Abstract: Cell spheroids bridge the discontinuity between in vitro systems and in vivo animal models. However, inducing cell spheroids by nanomaterials remains an inefficient and poorly understood process. ...Cell spheroids bridge the discontinuity between in vitro systems and in vivo animal models. However, inducing cell spheroids by nanomaterials remains an inefficient and poorly understood process. Here we use cryogenic electron microscopy to determine the atomic structure of helical nanofibres self-assembled from enzyme-responsive D-peptides and fluorescent imaging to show that the transcytosis of D-peptides induces intercellular nanofibres/gels that potentially interact with fibronectin to enable cell spheroid formation. Specifically, D-phosphopeptides, being protease resistant, undergo endocytosis and endosomal dephosphorylation to generate helical nanofibres. On secretion to the cell surface, these nanofibres form intercellular gels that act as artificial matrices and facilitate the fibrillogenesis of fibronectins to induce cell spheroids. No spheroid formation occurs without endo- or exocytosis, phosphate triggers or shape switching of the peptide assemblies. This study-coupling transcytosis and morphological transformation of peptide assemblies-demonstrates a potential approach for regenerative medicine and tissue engineering.
History
DepositionDec 13, 2021-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25714.png

Downloads & links

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Map

FileDownload / File: emd_25714.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of NBD-ffsy filaments (class 1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.582
Minimum - Maximum-0.90195334 - 1.7996882
Average (Standard dev.)0.00024572338 (±0.052695274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : self-assemble NBD-ffsy nanotube

EntireName: self-assemble NBD-ffsy nanotube
Components
  • Complex: self-assemble NBD-ffsy nanotube
    • Protein or peptide: NBD-ffsy peptide

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Supramolecule #1: self-assemble NBD-ffsy nanotube

SupramoleculeName: self-assemble NBD-ffsy nanotube / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: NBD-ffsy peptide

MacromoleculeName: NBD-ffsy peptide / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: DEXTRO
Source (natural)Organism: Synthetic construct (others)
Molecular weightTheoretical: 796.783 Da
SequenceString:
(UQ4)(DPN)(DPN)(DSN)(DTY)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 3.0 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: 0.483 Å
Applied symmetry - Helical parameters - Δ&Phi: 35.77 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: OTHER / Details: map:map FSC and model:map FSC / Number images used: 677537
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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