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- EMDB-9232: Cryo-EM structure of human AA amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: 9232
TitleCryo-EM structure of human AA amyloid fibril
Map dataCryo-EM reconstruction of human Serum Amyloid A fibrils, extracted from diseased human kidney. The fibril shows a helical rise of 2.40 A, a helical twist of 180.79 degree and a resolution of 2.7 A.
Samplehuman AA amyloid fibril:
Serum amyloid A-1 protein
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
SourceHomo sapiens (human) / Human (human)
Methodhelical reconstruction / cryo EM / 2.7 Å resolution
AuthorsRennegarbe M / Liberta F / 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 ReportPDB-ID: 6mst

SummaryFull reportAbout validation report
DateDeposition: Oct 18, 2018 / Header (metadata) release: Aug 1, 2018 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6mst
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6mst
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9232.map.gz (map file in CCP4 format, 78733 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
270 pix
1.04 Å/pix.
= 280.8 Å
270 pix
1.04 Å/pix.
= 280.8 Å
270 pix
1.04 Å/pix.
= 280.8 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
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.23911723 - 0.5025357
Average (Standard dev.)0.00038090933 (0.009526984)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions270270270
Origin0.00.00.0
Limit269.0269.0269.0
Spacing270270270
CellA=B=C: 280.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z280.800280.800280.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.2390.5030.000

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Supplemental data

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Mask #1

Fileemd_9232_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire human AA amyloid fibril

EntireName: human AA amyloid fibril / Number of components: 2

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Component #1: protein, human AA amyloid fibril

ProteinName: human AA amyloid fibril / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (natural)Organ or tissue: kidney

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Component #2: protein, Serum amyloid A-1 protein

ProteinName: Serum amyloid A-1 protein / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 7.481154 kDa
SourceSpecies: Human (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 2.4 Å / Delta phi: 0.79 deg.
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 7
Support film15 mA
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -500.0 - -2500.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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