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

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Basic information

Entry
Database: EMDB / ID: EMD-8910
TitleCryo-EM structure of murine AA amyloid fibril
Map data
SampleAA amyloid fibril:
Serum amyloid A-2 protein
Function / homology
Function and homology information


response to stilbenoid / high-density lipoprotein particle / cytoplasmic microtubule / chemoattractant activity / G protein-coupled receptor binding / cell chemotaxis / acute-phase response / extracellular space
Serum amyloid A protein
Serum amyloid A-2 protein
Biological speciesMus musculus (house mouse) / Mouse (mice)
Methodhelical reconstruction / cryo EM / Resolution: 3 Å
AuthorsLiberta F / Fandrich M / Schmidt M
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG FA 456/15-1 Germany
German Research Foundation (DFG)DFG SCHM 3276/1 Germany
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 /
Abstract: Systemic AA amyloidosis is a worldwide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from the acute phase protein serum amyloid A. Here, ...Systemic AA amyloidosis is a worldwide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from the acute phase protein serum amyloid A. Here, we report the purification and electron cryo-microscopy analysis of amyloid fibrils from a mouse and a human patient with systemic AA amyloidosis. The obtained resolutions are 3.0 Å and 2.7 Å for the murine and human fibril, respectively. The two fibrils differ in fundamental properties, such as presence of right-hand or left-hand twisted cross-β sheets and overall fold of the fibril proteins. Yet, both proteins adopt highly similar β-arch conformations within the N-terminal ~21 residues. Our data demonstrate the importance of the fibril protein N-terminus for the stability of the analyzed amyloid fibril morphologies and suggest strategies of combating this disease by interfering with specific fibril polymorphs.
Validation ReportPDB-ID: 6dso

SummaryFull reportAbout validation report
History
DepositionJun 14, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseMar 13, 2019-
UpdateJan 15, 2020-
Current statusJan 15, 2020Processing site: RCSB / Status: Released

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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 modelsPDB-6dso
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8910.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 210 pix.
= 283.5 Å
1.35 Å/pix.
x 210 pix.
= 283.5 Å
1.35 Å/pix.
x 210 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 LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.17764086 - 0.34451205
Average (Standard dev.)0.0008869683 (±0.010962577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 283.5 Å
α=β=γ: 90.0 °

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-383-383-383
NX/NY/NZ768768768
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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Segmentation: #1

Fileemd_8910_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Map 2 of two independently refined half maps

Fileemd_8910_half_map_1.map
AnnotationMap 2 of two independently refined half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Map 1 of two independently refined half maps

Fileemd_8910_half_map_2.map
AnnotationMap 1 of two independently refined half maps
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: 20 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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