+Open data
-Basic information
Entry | Database: PDB / ID: 6x5i | |||||||||
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Title | Cryo-EM of peptide-like filament of 1-KMe3 | |||||||||
Components | 1-KMe3 peptide-like fibril | |||||||||
Keywords | PROTEIN FIBRIL / peptide-like fibril / helical symmetry | |||||||||
Function / homology | polypeptide(D) Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Wang, F. / Feng, Z. / Xu, B. / Egelman, E.H. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep Phys Sci / Year: 2020 Title: Artificial Intracellular Filaments. Authors: Zhaoqianqi Feng / Huaimin Wang / Fengbin Wang / Younghoon Oh / Cristina Berciu / Qiang Cui / Edward H Egelman / Bing Xu / Abstract: Intracellular protein filaments are ubiquitous for cellular functions, but forming bona fide biomimetic intracellular filaments of small molecules in living cells remains elusive. Here, we report the ...Intracellular protein filaments are ubiquitous for cellular functions, but forming bona fide biomimetic intracellular filaments of small molecules in living cells remains elusive. Here, we report the formation of self-limiting intracellular filaments of a small peptide via enzymatic morphological transition of a phosphorylated and trimethylated heterochiral tetrapeptide. Enzymatic dephosphorylation reduces repulsive intermolecular electrostatic interactions and converts the peptidic nanoparticles into filaments, which exhibit distinct types of cross-β structures with either C7 or C2 symmetries, with the hydrophilic C-terminal residues at the periphery of the helix. Macromolecular crowding promotes the peptide filaments to form bundles, which extend from the plasma membrane to nuclear membrane and hardly interact with endogenous components, including cytoskeletons. Stereochemistry and post-translational modification (PTM) of peptides are critical for generating the intracellular bundles. This work may offer a way to gain lost functions or to provide molecular insights for understanding normal and aberrant intracellular filaments. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6x5i.cif.gz | 170.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x5i.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6x5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x5i_validation.pdf.gz | 684 KB | Display | wwPDB validaton report |
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Full document | 6x5i_full_validation.pdf.gz | 717.8 KB | Display | |
Data in XML | 6x5i_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 6x5i_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/6x5i ftp://data.pdbj.org/pub/pdb/validation_reports/x5/6x5i | HTTPS FTP |
-Related structure data
Related structure data | 22051MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 7 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 10 / Rise per n subunits: 4.9 Å / Rotation per n subunits: 2.3 °) |
-Components
#1: Polypeptide(D) | Mass: 880.965 Da / Num. of mol.: 70 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) Has ligand of interest | Y | |
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-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: 1-KMe3 peptide-like fibril / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 2.3 ° / Axial rise/subunit: 4.9 Å / Axial symmetry: C7 |
3D reconstruction | Resolution: 4.3 Å / Resolution method: OTHER / Num. of particles: 108886 / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Symmetry type: HELICAL |