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- EMDB-8910: Cryo-EM structure of murine AA amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: 8910
TitleCryo-EM structure of murine AA amyloid fibril
Map dataCryo-EM reconstruction of murine Serum Amyloid A fibrils from diseased mouse spleen using Relion 2.1. The central 30% of the reconstruction is shown.
SampleAA amyloid fibril:
Serum amyloid A-2 protein
Function / homologySerum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / response to stilbenoid / high-density lipoprotein particle / cytoplasmic microtubule / G protein-coupled receptor binding / chemoattractant activity / cell chemotaxis / acute-phase response ...Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / response to stilbenoid / high-density lipoprotein particle / cytoplasmic microtubule / G protein-coupled receptor binding / chemoattractant activity / cell chemotaxis / acute-phase response / extracellular space / Serum amyloid A-2 protein
Function and homology information
SourceMus musculus (house mouse) / Mouse (mice)
Methodhelical reconstruction / cryo EM / 3 Å resolution
AuthorsLiberta 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: 6dso

SummaryFull reportAbout validation report
DateDeposition: Jun 14, 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: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6dso
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6dso
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8910.map.gz (map file in CCP4 format, 37045 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
210 pix
1.35 Å/pix.
= 283.5 Å
210 pix
1.35 Å/pix.
= 283.5 Å
210 pix
1.35 Å/pix.
= 283.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.17764086 - 0.34451205
Average (Standard dev.)0.0008869683 (0.010962577)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions210210210
Origin0.00.00.0
Limit209.0209.0209.0
Spacing210210210
CellA=B=C: 283.5 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z210210210
origin x/y/z0.0000.0000.000
length x/y/z283.500283.500283.500
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.1780.3450.001

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Supplemental data

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Mask #1

Fileemd_8910_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire AA amyloid fibril

EntireName: AA amyloid fibril / Number of components: 2

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Component #1: protein, AA amyloid fibril

ProteinName: AA amyloid fibril / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (natural)Organ or tissue: spleen

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

ProteinName: Serum amyloid A-2 protein / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 9.362094 kDa
SourceSpecies: Mouse (mice)

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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: 2.41 Å / Delta phi: 179.44 deg.
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 7
Support film20 mA, 0.25 mBar
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 90 %

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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: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1300.0 - -5500.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1063

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 3 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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