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

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Basic information

Entry
Database: PDB / ID: 7qv6
TitleAmyloid fibril from the antimicrobial peptide aurein 3.3
ComponentsAurein-3.3
KeywordsPROTEIN FIBRIL / antimicrobial peptide / amyloid / filament / cross-beta
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBuecker, R. / Seuring, C. / Cazey, C. / Veith, K. / Garcia-Alai, M. / Gruenewald, K. / Landau, M.
Funding support5items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Aurein-3.3
A: Aurein-3.3
E: Aurein-3.3
D: Aurein-3.3
C: Aurein-3.3
F: Aurein-3.3
H: Aurein-3.3
G: Aurein-3.3
K: Aurein-3.3
J: Aurein-3.3
I: Aurein-3.3
L: Aurein-3.3
N: Aurein-3.3
M: Aurein-3.3
Q: Aurein-3.3
P: Aurein-3.3
O: Aurein-3.3
R: Aurein-3.3


Theoretical massNumber of molelcules
Total (without water)32,40318
Polymers32,40318
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Aurein-3.3


Mass: 1800.171 Da / Num. of mol.: 18 / Source method: obtained synthetically
Source: (synth.) Ranoidea raniformis (blue-thighed treefrog)
References: UniProt: P82396

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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: aurein 3.3 / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
Molecular weightValue: 22.3 kDa/nm / Experimental value: NO
Source (natural)Organism: Ranoidea raniformis (blue-thighed treefrog)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Concentration refers to peptide monomer before fibrillation
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: wait time 15s after application, blot time 4s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 350 nm / Calibrated defocus max: 3100 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 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: 5514 / Details: Collected in movie-mode; 40 frames per exposure.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2EPU2.8.0.1256image acquisition
3DigitalMicrograph3.32.2403image acquisition
5RELION3.1.3CTF correctionInternal CTFFIND4
8UCSF ChimeraX1.3model fitting
9Coot0.9.3model fitting
11cryoSPARC2.3initial Euler assignmentHelical SGD initial model
12RELION3.1.3initial Euler assignment2D classes for helical parameter estimation
13RELION3.1.3final Euler assignment
14RELION3.1.3classification
15RELION3.1.33D reconstruction
16PHENIX1.19.1model refinement
17ISOLDE1model refinement
CTF correctionDetails: CTF refined after 3D reconstruction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.136 ° / Axial rise/subunit: 4.892 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 174291 / Details: 4 unique helical units per segment
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35289 / Symmetry type: HELICAL
Atomic model buildingB value: 78.37 / 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-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0112304
ELECTRON MICROSCOPYf_angle_d0.5353078
ELECTRON MICROSCOPYf_dihedral_angle_d9.395306
ELECTRON MICROSCOPYf_chiral_restr0.054396
ELECTRON MICROSCOPYf_plane_restr0.001360

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