Uperin / Uperin family / cytolysis in another organism / other organism cell membrane / defense response to Gram-positive bacterium / protein homodimerization activity / extracellular region / membrane / Uperin-3.5
Function and homology information
Biological species
Uperoleia mjobergii (Mjoberg's toadlet)
Method
ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
United States - Israel Binational Science Foundation (BSF)
2017280
Joachim Herz Stiftung
Add-on Fellowship
Citation
Journal: Nat Commun / Year: 2022 Title: The Cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils. Authors: Robert Bücker / Carolin Seuring / Cornelia Cazey / Katharina Veith / Maria García-Alai / Kay Grünewald / Meytal Landau / Abstract: The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties ...The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils of mated β-sheets at atomic resolution. Uperin 3.5 formed a 3-blade symmetrical propeller of nine peptides per fibril layer including tight β-sheet interfaces. This cross-β cryo-EM structure complements the cross-α fibril conformation previously determined by crystallography, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked β-sheets allowing a rounded compactness of the fibril. The kinked β-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked Segments) found in human functional amyloids.
Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: wait time 15s after application, blot time 4s
-
Electron microscopy imaging
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
Microscopy
Model: FEI TITAN KRIOS
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Average exposure time: 3 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11857 / Details: Collected in movie-mode; 45 frames per exposure.
EM imaging optics
Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Num. of particles selected: 2447463 / Details: 4 unique helical units per segment
3D reconstruction
Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215020 / Symmetry type: HELICAL
Atomic model building
B value: 59.34 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: CC Details: - Initial model building of a single helical layer using ChimeraX and Coot - Expansion to three layers, refinement in ISOLDE - Truncation of outer layers, re-expansion to three layers, ...Details: - Initial model building of a single helical layer using ChimeraX and Coot - Expansion to three layers, refinement in ISOLDE - Truncation of outer layers, re-expansion to three layers, refinement using phenix.real_space_refine
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
ELECTRONMICROSCOPY
f_bond_d
0.009
2547
ELECTRONMICROSCOPY
f_angle_d
0.388
3402
ELECTRONMICROSCOPY
f_dihedral_angle_d
3.636
351
ELECTRONMICROSCOPY
f_chiral_restr
0.056
468
ELECTRONMICROSCOPY
f_plane_restr
0.002
414
+
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