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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23483 | |||||||||
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Title | Cryo-EM of 1-protofilament of the KFE8 thinner nanotube | |||||||||
![]() | cryo-EM of 1-protofilament of the KFE8 thinner nanotube | |||||||||
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![]() | filament / self-assembly peptide filament / Cryo-EM / peptide fibril / nanotube / PROTEIN FIBRIL | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Wang F / Gnewou OM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Deterministic chaos in the self-assembly of β sheet nanotubes from an amphipathic oligopeptide. Authors: Fengbin Wang / Ordy Gnewou / Shengyuan Wang / Tomasz Osinski / Xiaobing Zuo / Edward H Egelman / Vincent P Conticello / ![]() Abstract: The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical ...The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical devices. These peptide assemblies have also been used as models for understanding biological processes, such as the pathological formation of amyloid. We investigate the assembly of an octapeptide sequence, Ac-FKFEFKFE-NH, motivated by prior studies that demonstrated that this amphipathic β strand peptide self-assembled into fibrils and biocompatible hydrogels. Using high-resolution cryoelectron microscopy (cryo-EM), we are able to determine the atomic structure for two different coexisting forms of the fibrils, containing four and five β sandwich protofilaments, respectively. Surprisingly, the inner walls in both forms are parallel β sheets, while the outer walls are antiparallel β sheets. Our results demonstrate the chaotic nature of peptide self-assembly and illustrate the importance of cryo-EM structural analysis to understand the complex phase behavior of these materials at near-atomic resolution. | |||||||||
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 | ![]() | 8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.4 KB 9.4 KB | Display Display | ![]() |
Images | ![]() | 102.6 KB | ||
Filedesc metadata | ![]() | 4.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lqeMC ![]() 7lqfC ![]() 7lqgC ![]() 7lqhC ![]() 7lqiC 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 1-protofilament of the KFE8 thinner nanotube | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 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 KFE8 nanotubes
Entire | Name: self-assembly KFE8 nanotubes |
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Components |
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-Supramolecule #1: self-assembly KFE8 nanotubes
Supramolecule | Name: self-assembly KFE8 nanotubes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: KFE8 peptide
Macromolecule | Name: KFE8 peptide / type: protein_or_peptide / ID: 1 / Number of copies: 72 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 1.16435 KDa |
Sequence | String: (5CR)KFEFKF(GMA) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 7.93 Å Applied symmetry - Helical parameters - Δ&Phi: -15.8 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Details: Model:Map FSC 0.38 cut off / Number images used: 64959 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |