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Yorodumi- EMDB-14771: Amyloid fibril from human systemic AA amyloidosis (vascular variant) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14771 | |||||||||
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Title | Amyloid fibril from human systemic AA amyloidosis (vascular variant) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Amyloids / Vascular AA / SAA / Cryo-EM / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information Scavenging by Class B Receptors / positive regulation of interleukin-1 production / lymphocyte chemotaxis / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of protein secretion / macrophage chemotaxis / cytoplasmic microtubule / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling ...Scavenging by Class B Receptors / positive regulation of interleukin-1 production / lymphocyte chemotaxis / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of protein secretion / macrophage chemotaxis / cytoplasmic microtubule / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / positive regulation of cell adhesion / endocytic vesicle lumen / neutrophil chemotaxis / positive regulation of cytokine production / acute-phase response / G protein-coupled receptor binding / TAK1-dependent IKK and NF-kappa-B activation / platelet activation / negative regulation of inflammatory response / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / Interleukin-4 and Interleukin-13 signaling / Amyloid fiber formation / extracellular exosome / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.56 Å | |||||||||
Authors | Banerjee S / Schmidt M / Faendrich M | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Amyloid fibril structure from the vascular variant of systemic AA amyloidosis. Authors: Sambhasan Banerjee / Julian Baur / Christoph Daniel / Peter Benedikt Pfeiffer / Manuel Hitzenberger / Lukas Kuhn / Sebastian Wiese / Johan Bijzet / Christian Haupt / Kerstin U Amann / Martin ...Authors: Sambhasan Banerjee / Julian Baur / Christoph Daniel / Peter Benedikt Pfeiffer / Manuel Hitzenberger / Lukas Kuhn / Sebastian Wiese / Johan Bijzet / Christian Haupt / Kerstin U Amann / Martin Zacharias / Bouke P C Hazenberg / Gunilla T Westermark / Matthias Schmidt / Marcus Fändrich / Abstract: Systemic AA amyloidosis is a debilitating protein misfolding disease in humans and animals. In humans, it occurs in two variants that are called 'vascular' and 'glomerular', depending on the main ...Systemic AA amyloidosis is a debilitating protein misfolding disease in humans and animals. In humans, it occurs in two variants that are called 'vascular' and 'glomerular', depending on the main amyloid deposition site in the kidneys. Using cryo electron microscopy, we here show the amyloid fibril structure underlying the vascular disease variant. Fibrils purified from the tissue of such patients are mainly left-hand twisted and contain two non-equal stacks of fibril proteins. They contrast in these properties to the fibrils from the glomerular disease variant which are right-hand twisted and consist of two structurally equal stacks of fibril proteins. Our data demonstrate that the different disease variants in systemic AA amyloidosis are associated with different fibril morphologies. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14771.map.gz | 8.4 MB | EMDB map data format | |
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Header (meta data) | emd-14771-v30.xml emd-14771.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14771_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_14771.png | 21.8 KB | ||
Filedesc metadata | emd-14771.cif.gz | 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14771 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14771 | HTTPS FTP |
-Validation report
Summary document | emd_14771_validation.pdf.gz | 481.8 KB | Display | EMDB validaton report |
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Full document | emd_14771_full_validation.pdf.gz | 481.4 KB | Display | |
Data in XML | emd_14771_validation.xml.gz | 11 KB | Display | |
Data in CIF | emd_14771_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14771 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14771 | HTTPS FTP |
-Related structure data
Related structure data | 7zkyMC 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_14771.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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
-Sample components
-Entire : Amyloid fibril from human systemic AA amyloidosis (vascular variant)
Entire | Name: Amyloid fibril from human systemic AA amyloidosis (vascular variant) |
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Components |
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-Supramolecule #1: Amyloid fibril from human systemic AA amyloidosis (vascular variant)
Supramolecule | Name: Amyloid fibril from human systemic AA amyloidosis (vascular variant) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Amyloid protein A
Macromolecule | Name: Amyloid protein A / 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: 7.775502 KDa |
Sequence | String: SFFSFLGEAF DGARDMWRAY SDMREANYIG SDKYFHARGN YDAAKRGPGG VWAAEAISDA RENIQRFF UniProtKB: Serum amyloid A-1 protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 42.84 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7zky: |