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

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Basic information

Entry
Database: PDB / ID: 6zch
TitleAmyloid fibril morphology II (ex vivo) from murine SAA1.1 protein.
ComponentsSerum amyloid A-2 protein
KeywordsPROTEIN FIBRIL / systemic amyloidosis / misfolding disease / inflammation / prion
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBansal, A. / Schmidt, M. / Faendrich, M.
Funding support Germany, 6items
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, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
I: Serum amyloid A-2 protein
J: Serum amyloid A-2 protein
H: Serum amyloid A-2 protein
F: Serum amyloid A-2 protein
G: Serum amyloid A-2 protein
E: Serum amyloid A-2 protein
C: Serum amyloid A-2 protein
D: Serum amyloid A-2 protein
B: Serum amyloid A-2 protein
A: Serum amyloid A-2 protein
L: Serum amyloid A-2 protein
M: Serum amyloid A-2 protein
K: Serum amyloid A-2 protein
O: Serum amyloid A-2 protein
P: Serum amyloid A-2 protein
N: Serum amyloid A-2 protein
R: Serum amyloid A-2 protein
Q: Serum amyloid A-2 protein


Theoretical massNumber of molelcules
Total (without water)168,51818
Polymers168,51818
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area93700 Å2
ΔGint-275 kcal/mol
Surface area41240 Å2
MethodPISA

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Components

#1: Protein
Serum amyloid A-2 protein /


Mass: 9362.094 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P05367

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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: Serum amyloid A1 (SAA1) amyloid fibril / Type: COMPLEX / Details: ex vivo murine SAA amyloid fibril morphology II / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7 / Details: water
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 96 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 20 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9PHENIX1.16-3549model refinement
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.08807 ° / Axial rise/subunit: 4.80846 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 15530
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15505 / Symmetry type: HELICAL
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL / Target criteria: Correlation coefficient

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