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- EMDB-14771: Amyloid fibril from human systemic AA amyloidosis (vascular variant) -

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Basic information

Entry
Database: EMDB / ID: EMD-14771
TitleAmyloid fibril from human systemic AA amyloidosis (vascular variant)Amyloid
Map data
Sample
  • Complex: Amyloid fibril from human systemic AA amyloidosis (vascular variant)Amyloid
    • Protein or peptide: Amyloid protein A
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 / macrophage chemotaxis / regulation of protein secretion / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / positive regulation of cell adhesion ...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 / macrophage chemotaxis / regulation of protein secretion / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / positive regulation of cell adhesion / cytoplasmic microtubule / endocytic vesicle lumen / neutrophil chemotaxis / G protein-coupled receptor binding / positive regulation of cytokine production / acute-phase response / TAK1-dependent IKK and NF-kappa-B activation / negative regulation of inflammatory response / platelet activation / 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
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) / human (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.56 Å
AuthorsBanerjee S / Schmidt M / Faendrich M
Funding support1 items
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, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14771.png

Downloads & links

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Map

FileDownload / File: emd_14771.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0163
Minimum - Maximum-0.053856436 - 0.14575852
Average (Standard dev.)0.000722567 (±0.005809631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Amyloid fibril from human systemic AA amyloidosis (vascular variant)

EntireName: Amyloid fibril from human systemic AA amyloidosis (vascular variant)Amyloid
Components
  • Complex: Amyloid fibril from human systemic AA amyloidosis (vascular variant)Amyloid
    • Protein or peptide: Amyloid protein A

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Supramolecule #1: Amyloid fibril from human systemic AA amyloidosis (vascular variant)

SupramoleculeName: Amyloid fibril from human systemic AA amyloidosis (vascular variant)
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Amyloid protein A

MacromoleculeName: Amyloid protein A / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: human (human)
Molecular weightTheoretical: 7.775502 KDa
SequenceString:
SFFSFLGEAF DGARDMWRAY SDMREANYIG SDKYFHARGN YDAAKRGPGG VWAAEAISDA RENIQRFF

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.75 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.63 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77061
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

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

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