+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27688 | |||||||||||||||
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Title | Cryo-EM of NBD-ffsy filaments (class 2) | |||||||||||||||
Map data | Cryo-EM of NBD-ffsy filaments (class 2) | |||||||||||||||
Sample |
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Keywords | transcytosis / hydrogel / peptides / nanofibers / spheroids / self-assembly peptide filament / PROTEIN FIBRIL | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
Authors | Wang F / Guo J / Xu B / Egelman EH | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27688.map.gz | 42.4 MB | EMDB map data format | |
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Header (meta data) | emd-27688-v30.xml emd-27688.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_27688.png | 77.8 KB | ||
Others | emd_27688_half_map_1.map.gz emd_27688_half_map_2.map.gz | 318.8 MB 318.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27688 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27688 | HTTPS FTP |
-Validation report
Summary document | emd_27688_validation.pdf.gz | 772.3 KB | Display | EMDB validaton report |
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Full document | emd_27688_full_validation.pdf.gz | 771.8 KB | Display | |
Data in XML | emd_27688_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_27688_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27688 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27688 | HTTPS FTP |
-Related structure data
Related structure data | 8dstMC 7t6eC 8fofC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27688.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM of NBD-ffsy filaments (class 2) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half b
File | emd_27688_half_map_1.map | ||||||||||||
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Annotation | half b | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half a
File | emd_27688_half_map_2.map | ||||||||||||
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Annotation | half a | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : synthetic construct
Entire | Name: synthetic construct (others) |
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Components |
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-Supramolecule #1: synthetic construct
Supramolecule | Name: synthetic construct / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) / Synthetically produced: Yes |
-Macromolecule #1: NBD-ffsy peptide
Macromolecule | Name: NBD-ffsy peptide / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: DEXTRO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 796.783 Da |
Sequence | String: (UQ4)(DPN)(DPN)(DSN)(DTY) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.8 Å Applied symmetry - Helical parameters - Δ&Phi: -1.65 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 507178 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |