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- PDB-9ekc: cryo-EM of CL1 tube (outer) -

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Basic information

Entry
Database: PDB / ID: 9ekc
Titlecryo-EM of CL1 tube (outer)
ComponentsCL1 dimer
KeywordsPROTEIN FIBRIL / self-assembly peptide filament / Cryo-EM / helical filament
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang, F. / Gnewou, O. / Tuachi, A. / Egelman, E.H. / Conticello, V.P.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CL1 dimer
z: CL1 dimer
B: CL1 dimer
0: CL1 dimer
C: CL1 dimer
1: CL1 dimer
D: CL1 dimer
2: CL1 dimer
E: CL1 dimer
3: CL1 dimer
F: CL1 dimer
4: CL1 dimer
G: CL1 dimer
5: CL1 dimer
H: CL1 dimer
6: CL1 dimer
I: CL1 dimer
7: CL1 dimer
J: CL1 dimer
8: CL1 dimer
K: CL1 dimer
9: CL1 dimer
L: CL1 dimer
AA: CL1 dimer
M: CL1 dimer
BA: CL1 dimer
N: CL1 dimer
CA: CL1 dimer
O: CL1 dimer
DA: CL1 dimer
P: CL1 dimer
EA: CL1 dimer
Q: CL1 dimer
FA: CL1 dimer
R: CL1 dimer
GA: CL1 dimer
S: CL1 dimer
HA: CL1 dimer
T: CL1 dimer
IA: CL1 dimer
U: CL1 dimer
JA: CL1 dimer
V: CL1 dimer
KA: CL1 dimer
W: CL1 dimer
LA: CL1 dimer
X: CL1 dimer
MA: CL1 dimer
Y: CL1 dimer
NA: CL1 dimer
Z: CL1 dimer
OA: CL1 dimer
a: CL1 dimer
PA: CL1 dimer
b: CL1 dimer
QA: CL1 dimer
c: CL1 dimer
RA: CL1 dimer
d: CL1 dimer
SA: CL1 dimer
e: CL1 dimer
TA: CL1 dimer
f: CL1 dimer
UA: CL1 dimer
g: CL1 dimer
VA: CL1 dimer
h: CL1 dimer
WA: CL1 dimer
i: CL1 dimer
XA: CL1 dimer
j: CL1 dimer
YA: CL1 dimer
k: CL1 dimer
ZA: CL1 dimer
l: CL1 dimer
aA: CL1 dimer
m: CL1 dimer
bA: CL1 dimer
n: CL1 dimer
cA: CL1 dimer
o: CL1 dimer
dA: CL1 dimer
p: CL1 dimer
eA: CL1 dimer
q: CL1 dimer
fA: CL1 dimer
r: CL1 dimer
gA: CL1 dimer
s: CL1 dimer
hA: CL1 dimer
t: CL1 dimer
iA: CL1 dimer
u: CL1 dimer
jA: CL1 dimer
v: CL1 dimer
kA: CL1 dimer
w: CL1 dimer
lA: CL1 dimer
x: CL1 dimer
mA: CL1 dimer
y: CL1 dimer
nA: CL1 dimer


Theoretical massNumber of molelcules
Total (without water)150,840102
Polymers150,840102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
CL1 dimer


Mass: 1478.825 Da / Num. of mol.: 102 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: CL1 tube / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 109.67 ° / Axial rise/subunit: 2.04 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24736 / Symmetry type: HELICAL
RefinementHighest resolution: 3.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410812
ELECTRON MICROSCOPYf_angle_d0.86114382
ELECTRON MICROSCOPYf_dihedral_angle_d6.4411530
ELECTRON MICROSCOPYf_chiral_restr0.0291734
ELECTRON MICROSCOPYf_plane_restr0.0071734

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