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- EMDB-53573: Murine AA amyloid fibril morphology III (AA III) -

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Basic information

Entry
Database: EMDB / ID: EMD-53573
TitleMurine AA amyloid fibril morphology III (AA III)
Map data
Sample
  • Complex: Amyloid fibril containing SAA peptides
    • Protein or peptide: Serum amyloid A-2 protein
KeywordsAmyloid fibril / AA amyloidosis / systemic amyloidosis / AApoAII amyloidosis / misfolfing disease / protein aggregation / 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
AuthorsAndreotti G / Schmidt M / Faendrich M
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)1279/Z03 Germany
German Research Foundation (DFG)A03 Germany
CitationJournal: J Mol Biol / Year: 2025
Title: Cryo-EM Observation of AA Amyloid Fibrils in Mouse Model of Systemic AApoAII Amyloidosis.
Authors: Giada Andreotti / Keichii Higuchi / Matthias Schmidt / Marcus Fändrich /
Abstract: The co-deposition of amyloid fibrils from different precursor proteins is a topic of increasing relevance for protein misfolding diseases. Using cryo-electron microscopy (cryo-EM), we here determined ...The co-deposition of amyloid fibrils from different precursor proteins is a topic of increasing relevance for protein misfolding diseases. Using cryo-electron microscopy (cryo-EM), we here determined the structures of two serum amyloid A (SAA) protein-derived amyloid fibril morphologies that were extracted from a mouse strain that is primarily known to be associated with apolipoprotein A-II-derived amyloid fibrils. The two fibril morphologies show the same protomer conformation as in previously reported ex vivo amyloid fibrils from SAA protein but a different relative arrangement of fibril protein stacks. These data establish that serum amyloid A-derived amyloid fibrils share the same fibril protein fold in different mouse strains and disease contexts.
History
DepositionMay 8, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53573.png

Downloads & links

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Map

FileDownload / File: emd_53573.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.042014923 - 0.07255008
Average (Standard dev.)0.00010530845 (±0.0016988923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53573_msk_1.map
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Additional map: #1

Fileemd_53573_additional_1.map
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Half map: #2

Fileemd_53573_half_map_1.map
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Half map: #1

Fileemd_53573_half_map_2.map
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Sample components

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Entire : Amyloid fibril containing SAA peptides

EntireName: Amyloid fibril containing SAA peptides
Components
  • Complex: Amyloid fibril containing SAA peptides
    • Protein or peptide: Serum amyloid A-2 protein

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Supramolecule #1: Amyloid fibril containing SAA peptides

SupramoleculeName: Amyloid fibril containing SAA peptides / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse) / Organ: liver

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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: 12 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.622629 KDa
SequenceString:
GFFSFIGEAF QGAGDMWRAY TDMKEAGWKD GDKYFHARGN YDAAQRGPGG VWAAEKISDA RESFQEFFGR GHEDTMADQE ANRHGRSGK DPNYYRPPGL PAKY

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: 95 % / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.26 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 2034
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9r4z:
Murine AA amyloid fibril morphology III (AA III)

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