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Open data
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Basic information
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Title | IAPP S20G growth-phase fibril polymorph 4PF-CU | |||||||||
![]() | CryoEM map for 6-week aged IAPP-S20G 4PF-CU fibrils | |||||||||
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![]() | Amyloid / fibril / helical / cross-beta / Amylin / polymorph / islet / PROTEIN FIBRIL / Diabetes | |||||||||
Function / homology | ![]() amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / bone resorption ...amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / Regulation of gene expression in beta cells / negative regulation of protein-containing complex assembly / bone resorption / sensory perception of pain / positive regulation of calcium-mediated signaling / osteoclast differentiation / hormone activity / cell-cell signaling / amyloid-beta binding / G alpha (s) signalling events / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of apoptotic process / Amyloid fiber formation / signaling receptor binding / lipid binding / apoptotic process / signal transduction / extracellular space / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Wilkinson M / Xu Y / Gallardo R / Radford SE / Ranson NA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural evolution of fibril polymorphs during amyloid assembly. Authors: Martin Wilkinson / Yong Xu / Dev Thacker / Alexander I P Taylor / Declan G Fisher / Rodrigo U Gallardo / Sheena E Radford / Neil A Ranson / ![]() Abstract: Cryoelectron microscopy (cryo-EM) has provided unprecedented insights into amyloid fibril structures, including those associated with disease. However, these structures represent the endpoints of ...Cryoelectron microscopy (cryo-EM) has provided unprecedented insights into amyloid fibril structures, including those associated with disease. However, these structures represent the endpoints of long assembly processes, and their relationship to fibrils formed early in assembly is unknown. Consequently, whether different fibril architectures, with potentially different pathological properties, form during assembly remains unknown. Here, we used cryo-EM to determine structures of amyloid fibrils at different times during in vitro fibrillation of a disease-related variant of human islet amyloid polypeptide (IAPP-S20G). Strikingly, the fibrils formed in the lag, growth, and plateau phases have different structures, with new forms appearing and others disappearing as fibrillation proceeds. A time course with wild-type hIAPP also shows fibrils changing with time, suggesting that this is a general property of IAPP amyloid assembly. The observation of transiently populated fibril structures has implications for understanding amyloid assembly mechanisms with potential new insights into amyloid progression in disease. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.4 KB 18.4 KB | Display Display | ![]() |
Images | ![]() | 71.8 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 96.5 MB 96.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8az3MC ![]() 8awtC ![]() 8az0C ![]() 8az1C ![]() 8az2C ![]() 8az4C ![]() 8az5C ![]() 8az6C ![]() 8az7C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | CryoEM map for 6-week aged IAPP-S20G 4PF-CU fibrils | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: halfmap1
File | emd_15731_half_map_1.map | ||||||||||||
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Annotation | halfmap1 | ||||||||||||
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Density Histograms |
-Half map: halfmap2
File | emd_15731_half_map_2.map | ||||||||||||
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Annotation | halfmap2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : IAPP S20G growth-phase fibril polymorph 4PF-CU
Entire | Name: IAPP S20G growth-phase fibril polymorph 4PF-CU |
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Components |
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-Supramolecule #1: IAPP S20G growth-phase fibril polymorph 4PF-CU
Supramolecule | Name: IAPP S20G growth-phase fibril polymorph 4PF-CU / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: In vitro fibril growth for 6 weeks at room temperature |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Islet amyloid polypeptide
Macromolecule | Name: Islet amyloid polypeptide / type: protein_or_peptide / ID: 1 / Details: Synthesised with C-terminal amidation / Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3.877286 KDa |
Sequence | String: KCNTATCATQ RLANFLVHSG NNFGAILSST NVGSNTY(NH2) UniProtKB: Islet amyloid polypeptide |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.12 mg/mL |
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Buffer | pH: 6.8 / Component - Concentration: 20.0 mM / Component - Formula: NH3CH3CO2 / Component - Name: ammonium acetate |
Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 6s blot. |
Details | Fibrillation conditions: 30 uM monomeric IAPP-S20G, quiescent at room temp for 6 weeks |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 2350 / Average exposure time: 5.0 sec. / Average electron dose: 39.0 e/Å2 Details: 1204 raw EER frames were collected per image and combined into 30 fractions for processing |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 2.4 Å Applied symmetry - Helical parameters - Δ&Phi: 179.11 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 6895 |
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Segment selection | Number selected: 842792 Details: Manually picked a subset of images to train a model for automatic fibril segment picking in crYOLO |
Startup model | Type of model: INSILICO MODEL Details: Model generated from 2D class averages using relion_helix_inimodel2d |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 4.0) |