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- EMDB-14168: Amyloid fibril from the antimicrobial peptide aurein 3.3 -

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Basic information

Entry
Database: EMDB / ID: EMD-14168
TitleAmyloid fibril from the antimicrobial peptide aurein 3.3Amyloid
Map data
Sample
  • Complex: aurein 3.3
    • Protein or peptide: Aurein-3.3
Function / homologyAurein antibiotic peptide family / Aurein-like antibiotic peptide / defense response to bacterium / extracellular region / Aurein-3.3
Function and homology information
Biological speciesRanoidea raniformis (blue-thighed treefrog)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBuecker R / Seuring C / Cazey C / Veith K / Garcia-Alai M / Gruenewald K / Landau M
Funding support5 items
OrganizationGrant numberCountry
Other governmentLOM2018
Israel Science Foundation2111/20
Israel Ministry of Science and Technology3-15517
United States - Israel Binational Science Foundation (BSF)2017280
Joachim Herz StiftungAdd-on Fellowship
CitationJournal: 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.
History
DepositionJan 19, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14168.png

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Map

FileDownload / File: emd_14168.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 328 pix.
= 278.8 Å		0.85 Å/pix.
x 328 pix.
= 278.8 Å		0.85 Å/pix.
x 328 pix.
= 278.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.029938202 - 0.06529757
Average (Standard dev.)8.247845e-05 (±0.002902022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 278.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14168_msk_1.map
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Additional map: #1

Fileemd_14168_additional_1.map
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Half map: #2

Fileemd_14168_half_map_1.map
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Half map: #1

Fileemd_14168_half_map_2.map
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Sample components

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Entire : aurein 3.3

EntireName: aurein 3.3
Components
  • Complex: aurein 3.3
    • Protein or peptide: Aurein-3.3

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Supramolecule #1: aurein 3.3

SupramoleculeName: aurein 3.3 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ranoidea raniformis (blue-thighed treefrog)
Molecular weightTheoretical: 22.3 kDa/nm

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Macromolecule #1: Aurein-3.3

MacromoleculeName: Aurein-3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Ranoidea raniformis (blue-thighed treefrog)
Molecular weightTheoretical: 1.800171 KDa
SequenceString:
GLFDIVKKIA GHIVSSI

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration5 mg/mL
BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: wait time 15s after application, blot time 4s.
DetailsConcentration refers to peptide monomer before fibrillation

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.1 µm / Calibrated defocus min: 0.35000000000000003 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5514 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 / Details: Collected in movie-mode; 40 frames per exposure.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 174291 / Details: 4 unique helical units per segment
CTF correctionSoftware - Name: RELION (ver. 3.1.3) / Software - details: Internal CTFFIND4 / Details: CTF refined after 3D reconstruction
Startup modelType of model: NONE
Details: Ab-initio initial model from stochastic gradient descent with fixed helical parameters estimated from two-dimensional class averages.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1.3)
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.892 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.136 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 35289
FSC plot (resolution estimation)

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Atomic model buiding 1

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
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 78.37 / Target criteria: CC
Output model

PDB-7qv6:
Amyloid fibril from the antimicrobial peptide aurein 3.3

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