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

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9r4z
TitleMurine AA amyloid fibril morphology III (AA III)
ComponentsSerum amyloid A-2 protein
KeywordsPROTEIN FIBRIL / Amyloid fibril / AA amyloidosis / systemic amyloidosis / AApoAII amyloidosis / misfolfing disease / protein aggregation
Function / homology
Function and homology information


response to stilbenoid / high-density lipoprotein particle / cytoplasmic microtubule / acute-phase response / G protein-coupled receptor binding
Similarity search - Function
Serum amyloid A protein / : / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins
Similarity search - Domain/homology
Serum amyloid A-2 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAndreotti, G. / Schmidt, M. / Faendrich, M.
Funding support Germany, 2items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum amyloid A-2 protein
B: Serum amyloid A-2 protein
C: Serum amyloid A-2 protein
D: Serum amyloid A-2 protein
E: Serum amyloid A-2 protein
F: Serum amyloid A-2 protein
G: Serum amyloid A-2 protein
H: Serum amyloid A-2 protein
I: Serum amyloid A-2 protein
L: Serum amyloid A-2 protein
M: Serum amyloid A-2 protein
N: Serum amyloid A-2 protein


Theoretical massNumber of molelcules
Total (without water)139,47212
Polymers139,47212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Serum amyloid A-2 protein


Mass: 11622.629 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P05367
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Amyloid fibril containing SAA peptides / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Organ: liver
Buffer solutionpH: 7 / Details: water
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 42.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9RELION5initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
13Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.26 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C2
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2034 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL

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