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- EMDB-48119: cryo-EM of CL1 tube (outer) -

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Basic information

Entry
Database: EMDB / ID: EMD-48119
Titlecryo-EM of CL1 tube (outer)
Map dataouter tube
Sample
  • Complex: CL1 tube
    • Protein or peptide: CL1 dimer
Keywordsself-assembly peptide filament / Cryo-EM / helical filament / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang F / Gnewou O / Tuachi A / Egelman EH / Conticello VP
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
CitationJournal: Angew Chem Int Ed Engl / Year: 2025
Title: Amphipathic Antimicrobial Peptides Illuminate a Reciprocal Relationship Between Self-assembly and Cytolytic Activity.
Authors: Breana Laguera / Martina M Golden / Fengbin Wang / Ordy Gnewou / Abraham Tuachi / Edward H Egelman / William M Wuest / Vincent P Conticello /
Abstract: Amphipathic character, encoded within the polar sequence patterns of antimicrobial peptides, is a critical structural feature that influences membrane disruptive behavior. Similarly, polar sequence ...Amphipathic character, encoded within the polar sequence patterns of antimicrobial peptides, is a critical structural feature that influences membrane disruptive behavior. Similarly, polar sequence patterns induce self-assembly of amphipathic peptides, which results in the formation of ordered supramolecular structures. The relationship between self-assembly and membrane activity remains an open question of relevance for the development of effective antimicrobial peptides. Here, we report the structural investigation of a class of lytic peptides that self-assemble into filamentous nanomaterials. CryoEM analysis was employed to determine the structure of one of the filaments, which revealed that the peptides are self-assembled into a bilayer nanotube, in which the interaction between layers of amphipathic α-helices was mediated through hydrophobic interactions. The relative stability of the filament peptide assemblies depended on the influence of sequence modifications on the helical conformation. Antimicrobial assays indicated that cytolytic activity was associated with dynamic disassociation of the filamentous assemblies under the assay conditions. Structural modifications of the peptides that stabilized the filaments abrogated lytic activity. These results illuminate a reciprocal relationship between self-assembly and antimicrobial activity in this class of amphipathic peptides and that reversible assembly was critical for the observation of biological activity.
History
DepositionDec 2, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48119.png

Downloads & links

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Map

FileDownload / File: emd_48119.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationouter tube
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: 0.287
Minimum - Maximum-0.15288304 - 0.555415
Average (Standard dev.)0.004918098 (±0.03017008)
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 °

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Supplemental data

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Half map: half A

Fileemd_48119_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_48119_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CL1 tube

EntireName: CL1 tube
Components
  • Complex: CL1 tube
    • Protein or peptide: CL1 dimer

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Supramolecule #1: CL1 tube

SupramoleculeName: CL1 tube / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: CL1 dimer

MacromoleculeName: CL1 dimer / type: protein_or_peptide / ID: 1 / Number of copies: 102 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.478825 KDa
SequenceString:
FLGALFRALS RLL

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.04 Å
Applied symmetry - Helical parameters - Δ&Phi: 109.67 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24736
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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