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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21816 | |||||||||
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Title | Cryo-EM of Form 2 like peptide filament, 29-20-2 | |||||||||
![]() | Cryo-EM of Form 2 like peptide filament, 29-20-2 | |||||||||
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![]() | filament / self-assembly peptide filament / Cryo-EM / PROTEIN FIBRIL | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Wang F / Gnewou OM | |||||||||
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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 16.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.5 KB 10.5 KB | Display Display | ![]() |
Images | ![]() | 129.6 KB | ||
Filedesc metadata | ![]() | 4.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 446.6 KB | Display | ![]() |
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Full document | ![]() | 446.2 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wl7MC ![]() 6wkxC ![]() 6wkyC ![]() 6wl0C ![]() 6wl1C ![]() 6wl8C ![]() 6wl9C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM of Form 2 like peptide filament, 29-20-2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : self-assembly peptide filament, 29-20-2
Entire | Name: self-assembly peptide filament, 29-20-2 |
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Components |
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-Supramolecule #1: self-assembly peptide filament, 29-20-2
Supramolecule | Name: self-assembly peptide filament, 29-20-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: synthetic peptide |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: peptide 29-20-2
Macromolecule | Name: peptide 29-20-2 / type: protein_or_peptide / ID: 1 / Number of copies: 150 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.253769 KDa |
Sequence | String: QAEILEADAR ILRAYAEILK AHAEILKAQ |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 5.63 Å Applied symmetry - Helical parameters - Δ&Phi: 12.90 ° Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Details: Model:Map FSC 0.38 cut off and d99 / Number images used: 67941 |
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Startup model | Type of model: OTHER / Details: featureless cylinder |
Final angle assignment | Type: NOT APPLICABLE |