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- EMDB-11164: Amyloid fibril morphology II (ex vivo) from murine SAA1.1 protein. -

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Basic information

Entry
Database: EMDB / ID: EMD-11164
TitleAmyloid fibril morphology II (ex vivo) from murine SAA1.1 protein.
Map dataex vivo mSAA amyloid fibril morphology II
Sample
  • Complex: Serum amyloid A1 (SAA1) amyloid fibril
    • Protein or peptide: Serum amyloid A-2 protein
Keywordssystemic amyloidosis / misfolding disease / inflammation / prion / PROTEIN FIBRIL
Function / homologySerum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins / response to stilbenoid / high-density lipoprotein particle / acute-phase response / Serum amyloid A-2 protein
Function and homology information
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBansal A / Schmidt M
Funding support Germany, 6 items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG SCHM 3276/1 Germany
German Research Foundation (DFG)DFG FA 456/15 Germany
German Research Foundation (DFG)DFG FA 456/23 Germany
German Research Foundation (DFG)DFG FA 456/27 Germany
German Research Foundation (DFG)DFG HA 7138/3 Germany
German Research Foundation (DFG)DFG HA 7138/2 Germany
CitationJournal: Nat Commun / Year: 2021
Title: AA amyloid fibrils from diseased tissue are structurally different from in vitro formed SAA fibrils.
Authors: Akanksha Bansal / Matthias Schmidt / Matthies Rennegarbe / Christian Haupt / Falk Liberta / Sabrina Stecher / Ioana Puscalau-Girtu / Alexander Biedermann / Marcus Fändrich /
Abstract: Systemic AA amyloidosis is a world-wide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from serum amyloid A (SAA) protein. Using cryo ...Systemic AA amyloidosis is a world-wide occurring protein misfolding disease of humans and animals. It arises from the formation of amyloid fibrils from serum amyloid A (SAA) protein. Using cryo electron microscopy we here show that amyloid fibrils which were purified from AA amyloidotic mice are structurally different from fibrils formed from recombinant SAA protein in vitro. Ex vivo amyloid fibrils consist of fibril proteins that contain more residues within their ordered parts and possess a higher β-sheet content than in vitro fibril proteins. They are also more resistant to proteolysis than their in vitro formed counterparts. These data suggest that pathogenic amyloid fibrils may originate from proteolytic selection, allowing specific fibril morphologies to proliferate and to cause damage to the surrounding tissue.
History
DepositionJun 11, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zch
  • Surface level: 13
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zch
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11164.png

Downloads & links

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Map

FileDownload / File: emd_11164.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationex vivo mSAA amyloid fibril morphology II
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.35 Å/pix.
x 120 pix.
= 162. Å		1.35 Å/pix.
x 120 pix.
= 162. Å		1.35 Å/pix.
x 120 pix.
= 162. 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 13.0 / Movie #1: 13
Minimum - Maximum-21.414960000000001 - 40.622909999999997
Average (Standard dev.)0.2781334 (±2.294398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 162.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z162.000162.000162.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ120120120
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-21.41540.6230.278

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Supplemental data

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Half map: ex vivo mSAA amyloid fibril morphology II (half map II)

Fileemd_11164_half_map_1.map
Annotationex vivo mSAA amyloid fibril morphology II (half map II)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ex vivo mSAA amyloid fibril morphology II (half map I)

Fileemd_11164_half_map_2.map
Annotationex vivo mSAA amyloid fibril morphology II (half map I)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Serum amyloid A1 (SAA1) amyloid fibril

EntireName: Serum amyloid A1 (SAA1) amyloid fibril
Components
  • Complex: Serum amyloid A1 (SAA1) amyloid fibril
    • Protein or peptide: Serum amyloid A-2 protein

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Supramolecule #1: Serum amyloid A1 (SAA1) amyloid fibril

SupramoleculeName: Serum amyloid A1 (SAA1) amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: ex vivo murine SAA amyloid fibril morphology II
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Serum amyloid A-2 protein

MacromoleculeName: Serum amyloid A-2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.362094 KDa
SequenceString:
GFFSFIGEAF QGAGDMWRAY TDMKEAGWKD GDKYFHARGN YDAAQRGPGG VWAAEKISDA RESFQEFFGR GHEDTMADQE ANR

UniProtKB: Serum amyloid A-2 protein

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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 / Details: water
VitrificationCryogen name: ETHANE / Chamber humidity: 96 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.80846 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.08807 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 15505
Segment selectionNumber selected: 15530
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Target criteria: Correlation coefficient
Output model

PDB-6zch:
Amyloid fibril morphology II (ex vivo) from murine SAA1.1 protein.

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