+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14167 | ||||||||||||||||||
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Title | Amyloid fibril from the antimicrobial peptide uperin 3.5 | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Function / homology | 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 | helical reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||||||||
Authors | Buecker R / Seuring C / Cazey C / Veith K / Garcia-Alai M / Gruenewald K / Landau M | ||||||||||||||||||
Funding support | 5 items
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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. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14167.map.gz | 125.9 MB | EMDB map data format | |
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Header (meta data) | emd-14167-v30.xml emd-14167.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14167_fsc.xml | 11.6 KB | Display | FSC data file |
Images | emd_14167.png | 161.4 KB | ||
Masks | emd_14167_msk_1.map | 134.6 MB | Mask map | |
Others | emd_14167_half_map_1.map.gz emd_14167_half_map_2.map.gz | 105.7 MB 105.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14167 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14167 | HTTPS FTP |
-Validation report
Summary document | emd_14167_validation.pdf.gz | 715.6 KB | Display | EMDB validaton report |
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Full document | emd_14167_full_validation.pdf.gz | 715.2 KB | Display | |
Data in XML | emd_14167_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | emd_14167_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14167 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14167 | HTTPS FTP |
-Related structure data
Related structure data | 7qv5MC 7qv6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14167.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14167_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14167_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14167_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : uperin 3.5
Entire | Name: uperin 3.5 |
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Components |
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-Supramolecule #1: uperin 3.5
Supramolecule | Name: uperin 3.5 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Uperoleia mjobergii (Mjoberg's toadlet) |
Molecular weight | Theoretical: 33.0 kDa/nm |
-Macromolecule #1: Uperin-3.5
Macromolecule | Name: Uperin-3.5 / type: protein_or_peptide / ID: 1 / Number of copies: 27 / Enantiomer: LEVO |
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Source (natural) | Organism: Uperoleia mjobergii (Mjoberg's toadlet) |
Molecular weight | Theoretical: 1.782181 KDa |
Sequence | String: GVGDLIRKAV SVIKNIV(NH2) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: wait time 15s after application, blot time 4s. |
Details | Concentration refers to peptide monomer before fibrillation |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11857 / Average exposure time: 3.0 sec. / Average electron dose: 40.0 e/Å2 / Details: Collected in movie-mode; 45 frames per exposure. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.1 µm / Calibrated defocus min: 0.35000000000000003 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-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 |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 59.34 / Target criteria: CC |
Output model | PDB-7qv5: |