+Open data
-Basic information
Entry | Database: PDB / ID: 7rx4 | ||||||||||||
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Title | Cryo-EM reconstruction of AS2 nanotube (Form II like) | ||||||||||||
Components | AS2 peptide | ||||||||||||
Keywords | STRUCTURAL PROTEIN / helical symmetry / peptide nanotube / self-assembly | ||||||||||||
Biological species | Synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Wang, F. / Gnewou, O.M. / Solemanifar, A. / Xu, C. / Egelman, E.H. / Conticello, V.P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Chem Rev / Year: 2022 Title: Cryo-EM of Helical Polymers. Authors: Fengbin Wang / Ordy Gnewou / Armin Solemanifar / Vincent P Conticello / Edward H Egelman / Abstract: While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, ...While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior. | ||||||||||||
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 | 7rx4.cif.gz | 18.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rx4.ent.gz | 11.3 KB | Display | PDB format |
PDBx/mmJSON format | 7rx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rx4_validation.pdf.gz | 663.9 KB | Display | wwPDB validaton report |
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Full document | 7rx4_full_validation.pdf.gz | 663.3 KB | Display | |
Data in XML | 7rx4_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 7rx4_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/7rx4 ftp://data.pdbj.org/pub/pdb/validation_reports/rx/7rx4 | HTTPS FTP |
-Related structure data
Related structure data | 24724MC 7rx5C 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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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 30 / Rise per n subunits: 1.907 Å / Rotation per n subunits: 124.3 °) |
-Components
#1: Protein/peptide | Mass: 3224.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
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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: AS2 peptide nanotube / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Synthetic construct (others) |
Buffer solution | pH: 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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 124.3 ° / Axial rise/subunit: 1.907 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: HELICAL |