+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33902 | ||||||||||||
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Title | Structure of hIAPP-TF-type1 | ||||||||||||
Map data | hIAPP-WF-type1 | ||||||||||||
Sample |
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Keywords | amylin / PROTEIN FIBRIL | ||||||||||||
Function / homology | Function and homology information amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / positive regulation of protein kinase A signaling / negative regulation of osteoclast differentiation / 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 / positive regulation of protein kinase A signaling / negative regulation of osteoclast differentiation / 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 | Homo sapiens (human) | ||||||||||||
Method | helical reconstruction / Resolution: 3.2 Å | ||||||||||||
Authors | Li DG / Zhang XL / Wang YW / Zhu P | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: iScience / Year: 2022 Title: A new polymorphism of human amylin fibrils with similar protofilaments and a conserved core. Authors: Dongyu Li / Xueli Zhang / Youwang Wang / Haonan Zhang / Kai Song / Keyan Bao / Ping Zhu / Abstract: Pancreatic amyloid deposits composed of a fibrillar form of the human islet amyloid polypeptide (hIAPP) are the pathological hallmark of type 2 diabetes (T2D). Although various cryo-EM structures of ...Pancreatic amyloid deposits composed of a fibrillar form of the human islet amyloid polypeptide (hIAPP) are the pathological hallmark of type 2 diabetes (T2D). Although various cryo-EM structures of polymorphic hIAPP fibrils were reported, the underlying polymorphic mechanism of hIAPP remains elusive. Meanwhile, the structure of hIAPP fibrils with all residues visible in the fibril core is not available. Here, we report the full-length structures of two different polymorphs of hIAPP fibrils, namely slim form (SF, dimer) and thick form (TF, tetramer), formed in a salt-free environment, which share a similar ζ-shaped protofilament but differ in inter-protofilament interfaces. In the absence of salt, electrostatic interactions were found to play a dominant role in stabilizing the fibril structure, suggesting an antagonistic effect between electrostatic and hydrophobic interactions in different salt concentrations environments. Our results shed light on understanding the mechanism of amyloid fibril polymorphism. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33902.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-33902-v30.xml emd-33902.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33902_fsc.xml | 9.4 KB | Display | FSC data file |
Images | emd_33902.png | 63 KB | ||
Filedesc metadata | emd-33902.cif.gz | 4.6 KB | ||
Others | emd_33902_half_map_1.map.gz emd_33902_half_map_2.map.gz | 54.3 MB 54.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33902 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33902 | HTTPS FTP |
-Validation report
Summary document | emd_33902_validation.pdf.gz | 706 KB | Display | EMDB validaton report |
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Full document | emd_33902_full_validation.pdf.gz | 705.5 KB | Display | |
Data in XML | emd_33902_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_33902_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33902 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33902 | HTTPS FTP |
-Related structure data
Related structure data | 7yl3MC 7ykwC 7yl0C 7yl7C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33902.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | hIAPP-WF-type1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33902_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33902_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Islet amyloid polypeptide
Entire | Name: Islet amyloid polypeptide |
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Components |
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-Supramolecule #1: Islet amyloid polypeptide
Supramolecule | Name: Islet amyloid polypeptide / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) / Synthetically produced: Yes |
-Macromolecule #1: Islet amyloid polypeptide
Macromolecule | Name: Islet amyloid polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 3.908319 KDa |
Sequence | String: KCNTATCATQ RLANFLVHSS NNFGAILSST NVGSNT(TYC) UniProtKB: Islet amyloid polypeptide |
-Experimental details
-Structure determination
Processing | helical reconstruction |
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Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.8 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |