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- PDB-7zky: Amyloid fibril from human systemic AA amyloidosis (vascular variant) -

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Basic information

Entry
Database: PDB / ID: 7zky
TitleAmyloid fibril from human systemic AA amyloidosis (vascular variant)
ComponentsAmyloid protein A
KeywordsPROTEIN FIBRIL / Amyloids / Vascular AA / SAA / Cryo-EM
Function / homology
Function and homology information


Scavenging by Class B Receptors / lymphocyte chemotaxis / positive regulation of interleukin-1 production / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / macrophage chemotaxis / regulation of protein secretion / cytoplasmic microtubule / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling ...Scavenging by Class B Receptors / lymphocyte chemotaxis / positive regulation of interleukin-1 production / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / macrophage chemotaxis / regulation of protein secretion / cytoplasmic microtubule / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / endocytic vesicle lumen / neutrophil chemotaxis / positive regulation of cell adhesion / 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 / Interleukin-4 and Interleukin-13 signaling / G alpha (q) signalling events / Amyloid fiber formation / extracellular exosome / extracellular region
Similarity search - Function
Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins
Similarity search - Domain/homology
Serum amyloid A-1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsBanerjee, S. / Schmidt, M. / Faendrich, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionApr 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Amyloid protein A
A: Amyloid protein A
D: Amyloid protein A
C: Amyloid protein A
F: Amyloid protein A
E: Amyloid protein A
H: Amyloid protein A
G: Amyloid protein A
J: Amyloid protein A
I: Amyloid protein A
L: Amyloid protein A
K: Amyloid protein A


Theoretical massNumber of molelcules
Total (without water)93,30612
Polymers93,30612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area53510 Å2
ΔGint-237 kcal/mol
Surface area22630 Å2
MethodPISA

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Components

#1: Protein
Amyloid protein A / Amyloid fibril protein AA


Mass: 7775.502 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0DJI8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Amyloid fibril from human systemic AA amyloidosis (vascular variant)
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingAverage 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.63 ° / Axial rise/subunit: 4.75 Å / Axial symmetry: C1
3D reconstructionResolution: 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 buildingProtocol: AB INITIO MODEL

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