+Open data
-Basic information
Entry | Database: PDB / ID: 8fof | |||||||||||||||
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Title | Cryo-EM of BP-ffsy filaments | |||||||||||||||
Components | BP-ffsy | |||||||||||||||
Keywords | PROTEIN FIBRIL / transcytosis / hydrogel / peptides / nanofibers / spheroids / self-assembly peptide filament | |||||||||||||||
Function / homology | polypeptide(D) Function and homology information | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||||||||
Authors | Wang, F. / Guo, J. / Egelman, E.H. / Xu, B. | |||||||||||||||
Funding support | United States, 4items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fof.cif.gz | 9.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fof.ent.gz | 4.8 KB | Display | PDB format |
PDBx/mmJSON format | 8fof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fof_validation.pdf.gz | 950 KB | Display | wwPDB validaton report |
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Full document | 8fof_full_validation.pdf.gz | 949.5 KB | Display | |
Data in XML | 8fof_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 8fof_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/8fof ftp://data.pdbj.org/pub/pdb/validation_reports/fo/8fof | HTTPS FTP |
-Related structure data
Related structure data | 29348MC 7t6eC 8dstC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Symmetry | Helical symmetry: (Circular symmetry: 3 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 14 / Rise per n subunits: 2.11 Å / Rotation per n subunits: -54.79 °) |
-Components
#1: Polypeptide(D) | Mass: 742.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: BP-ffsy / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: synthetic construct (others) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -54.79 ° / Axial rise/subunit: 2.11 Å / Axial symmetry: C3 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 757253 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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