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- PDB-7zky: Amyloid fibril from human systemic AA amyloidosis (vascular variant) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zky | ||||||
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Title | Amyloid fibril from human systemic AA amyloidosis (vascular variant) | ||||||
![]() | Amyloid protein A | ||||||
![]() | PROTEIN FIBRIL / Amyloids / Vascular AA / SAA / Cryo-EM | ||||||
Function / homology | ![]() 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 / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / Interleukin-4 and Interleukin-13 signaling / Amyloid fiber formation / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.56 Å | ||||||
![]() | Banerjee, S. / Schmidt, M. / Faendrich, M. | ||||||
Funding support | 1items
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.2 KB | Display | ![]() |
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PDB format | ![]() | 96.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 736.1 KB | Display | ![]() |
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Full document | ![]() | 736.3 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14771MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 7775.502 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Amyloid fibril from human systemic AA amyloidosis (vascular variant) Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 10 sec. / Electron dose: 42.84 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: -1.63 ° / Axial rise/subunit: 4.75 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77061 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Num. of class averages: 1 / Symmetry type: HELICAL |
Atomic model building | Protocol: AB INITIO MODEL |