|Entry||Database: EMDB / ID: 9232|
|Title||Cryo-EM structure of human AA amyloid fibril|
|Map data||Cryo-EM reconstruction of human Serum Amyloid A fibrils, extracted from diseased human kidney. The fibril shows a helical rise of 2.40 A, a helical twist of 180.79 degree and a resolution of 2.7 A.|
|Sample||human AA amyloid fibril:|
Serum amyloid A-1 protein
|Function / homology||Scavenging by Class B Receptors / Interleukin-4 and Interleukin-13 signaling / Serum amyloid A proteins signature. / Serum amyloid A protein / Serum amyloid A protein / G alpha (i) signalling events / Formyl peptide receptors bind formyl peptides and many other ligands / G alpha (q) signalling events / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / Amyloid fiber formation ...Scavenging by Class B Receptors / Interleukin-4 and Interleukin-13 signaling / Serum amyloid A proteins signature. / Serum amyloid A protein / Serum amyloid A protein / G alpha (i) signalling events / Formyl peptide receptors bind formyl peptides and many other ligands / G alpha (q) signalling events / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / Amyloid fiber formation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / positive regulation of interleukin-1 secretion / lymphocyte chemotaxis / macrophage chemotaxis / high-density lipoprotein particle / regulation of protein secretion / cytoplasmic microtubule / positive regulation of cell adhesion / G protein-coupled receptor binding / chemoattractant activity / cell chemotaxis / endocytic vesicle lumen / positive regulation of cytokine secretion / neutrophil chemotaxis / negative regulation of inflammatory response / acute-phase response / receptor-mediated endocytosis / positive regulation of cytosolic calcium ion concentration / platelet activation / heparin binding / activation of MAPK activity / G protein-coupled receptor signaling pathway / cytokine-mediated signaling pathway / innate immune response / cellular protein metabolic process / extracellular space / extracellular exosome / extracellular region / Serum amyloid A-1 protein|
Function and homology information
|Source||Homo sapiens (human) / Human (human)|
|Method||helical reconstruction / cryo EM / 2.7 Å resolution|
|Authors||Rennegarbe M / Liberta F / Fandrich M / Schmidt M|
|Citation||Journal: Nat Commun / Year: 2019|
Title: Cryo-EM fibril structures from systemic AA amyloidosis reveal the species complementarity of pathological amyloids.
Authors: Falk Liberta / Sarah Loerch / Matthies Rennegarbe / Angelika Schierhorn / Per Westermark / Gunilla T Westermark / Bouke P C Hazenberg / Nikolaus Grigorieff / Marcus Fändrich / Matthias Schmidt
|Validation Report||PDB-ID: 6mst|
SummaryFull reportAbout validation report
|Date||Deposition: Oct 18, 2018 / Header (metadata) release: Aug 1, 2018 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||emd_9232.map.gz (map file in CCP4 format, 78733 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.04 Å|
CCP4 map header:
-Entire human AA amyloid fibril
|Entire||Name: human AA amyloid fibril / Number of components: 2|
-Component #1: protein, human AA amyloid fibril
|Protein||Name: human AA amyloid fibril / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (natural)||Organ or tissue: kidney|
-Component #2: protein, Serum amyloid A-1 protein
|Protein||Name: Serum amyloid A-1 protein / Number of Copies: 12 / Recombinant expression: No|
|Mass||Theoretical: 7.481154 kDa|
|Source||Species: Human (human)|
|Specimen||Specimen state: helical array / Method: cryo EM|
|Helical parameters||Axial symmetry: C1 (asymmetric) / Delta z: 2.4 Å / Delta phi: 0.79 deg.|
|Sample solution||Specimen conc.: 0.2 mg/ml / pH: 7|
|Support film||15 mA|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 95 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -500.0 - -2500.0 nm|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: helical reconstruction|
|3D reconstruction||Software: RELION / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF|
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