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- EMDB-23483: Cryo-EM of 1-protofilament of the KFE8 thinner nanotube -

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Basic information

Entry
Database: EMDB / ID: EMD-23483
TitleCryo-EM of 1-protofilament of the KFE8 thinner nanotube
Map datacryo-EM of 1-protofilament of the KFE8 thinner nanotube
Sample
  • Complex: self-assembly KFE8 nanotubes
    • Protein or peptide: KFE8 peptide
Keywordsfilament / self-assembly peptide filament / Cryo-EM / peptide fibril / nanotube / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang F / Gnewou OM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-DMR-1533958 United States
CitationJournal: Matter / Year: 2021
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
DepositionFeb 13, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.264
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.264
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lqe
  • Surface level: 0.264
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lqe
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23483.png

Downloads & links

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Map

FileDownload / File: emd_23483.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM of 1-protofilament of the KFE8 thinner nanotube
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.264 / Movie #1: 0.264
Minimum - Maximum-0.00023774995 - 1.0104212
Average (Standard dev.)0.002381838 (±0.025686206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.0001.0100.002

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Supplemental data

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Sample components

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Entire : self-assembly KFE8 nanotubes

EntireName: self-assembly KFE8 nanotubes
Components
  • Complex: self-assembly KFE8 nanotubes
    • Protein or peptide: KFE8 peptide

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Supramolecule #1: self-assembly KFE8 nanotubes

SupramoleculeName: self-assembly KFE8 nanotubes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: KFE8 peptide

MacromoleculeName: KFE8 peptide / type: protein_or_peptide / ID: 1 / Number of copies: 72 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.16435 KDa
SequenceString:
(5CR)KFEFKF(GMA)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied 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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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