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Open data
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Basic information
Entry | Database: PDB / ID: 6wl1 | ||||||
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Title | Cryo-EM of Form 1 related peptide filament, 36-31-3 | ||||||
![]() | peptide 36-31-3 | ||||||
![]() | PROTEIN FIBRIL / filament / self-assembly peptide filament / Cryo-EM | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å | ||||||
![]() | Wang, F. / Gnewou, O.M. / Modlin, C. / Egelman, E.H. / Conticello, V.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials. Authors: Fengbin Wang / Ordy Gnewou / Charles Modlin / Leticia C Beltran / Chunfu Xu / Zhangli Su / Puneet Juneja / Gevorg Grigoryan / Edward H Egelman / Vincent P Conticello / ![]() Abstract: The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of ...The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 300.7 KB | Display | ![]() |
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PDB format | ![]() | 257.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 954.3 KB | Display | ![]() |
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Full document | ![]() | 953.7 KB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 55.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 21815MC ![]() 6wkxC ![]() 6wkyC ![]() 6wl0C ![]() 6wl7C ![]() 6wl8C ![]() 6wl9C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 52 / Rise per n subunits: 2.5 Å / Rotation per n subunits: 124 °) |
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Components
#1: Protein/peptide | Mass: 4008.662 Da / Num. of mol.: 52 / 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 |
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Sample preparation
Component | Name: self-assembly peptide filament, 36-31-3 / Type: COMPLEX / Details: synthetic peptide / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: synthetic construct (others) |
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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: dev_2919: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Helical symmerty | Angular rotation/subunit: 124 ° / Axial rise/subunit: 2.5 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 4 Å / Resolution method: OTHER / Num. of particles: 66079 / Details: Model:Map FSC 0.38 cut off and d99 / Symmetry type: HELICAL |