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- PDB-6mst: Cryo-EM structure of human AA amyloid fibril -

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Basic information

Entry
Database: PDB / ID: 6mst
TitleCryo-EM structure of human AA amyloid fibril
ComponentsSerum amyloid A-1 protein
KeywordsPROTEIN FIBRIL / AA-amyloidosis / Serum Amyloid A / cross-beta / helical / protein fibril
Function / homologyScavenging 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
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 2.7 Å resolution
AuthorsLoerch, S. / Rennegarbe, M. / Liberta, F. / Grigorieff, N. / Fandrich, M. / Schmidt, M.
CitationJournal: 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
SummaryFull reportAbout validation report
DateDeposition: Oct 18, 2018 / Release: Mar 13, 2019

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Structure visualization

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Assembly

Deposited unit
A: Serum amyloid A-1 protein
B: Serum amyloid A-1 protein
C: Serum amyloid A-1 protein
E: Serum amyloid A-1 protein
D: Serum amyloid A-1 protein
F: Serum amyloid A-1 protein
H: Serum amyloid A-1 protein
I: Serum amyloid A-1 protein
J: Serum amyloid A-1 protein
K: Serum amyloid A-1 protein
L: Serum amyloid A-1 protein
G: Serum amyloid A-1 protein


Theoretical massNumber of molelcules
Total (without water)89,77412
Polyers89,77412
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide
Serum amyloid A-1 protein / / SAA


Mass: 7481.154 Da / Num. of mol.: 12 / 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 / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: human AA amyloid fibril / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organ: kidney / Organism: Homo sapiens (human)
Buffer solutionpH: 7
Buffer componentFormula: ddH2O
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 / Nominal defocus max: -2500 nm / Nominal defocus min: -500 nm / Cs: 2.7 mm / C2 aperture diameter: 5 microns
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 12 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2SerialEM3.5image acquisition
4Gctf1.06CTF correction
7PHENIX1.14-3219model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.14-3219model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0.79 deg. / Axial rise/subunit: 2.4 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 93025
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 91872 / Symmetry type: HELICAL
Atomic model buildingRef protocol: AB INITIO MODEL

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