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- PDB-6dso: Cryo-EM structure of murine AA amyloid fibril -

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Basic information

Entry
Database: PDB / ID: 6dso
TitleCryo-EM structure of murine AA amyloid fibril
ComponentsSerum amyloid A-2 protein
KeywordsPROTEIN FIBRIL / AA-amyloidosis / fibril / cross-beta / helical
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 Å
AuthorsLoerch, S. / Liberta, F. / Grigorieff, N. / Fandrich, M. / Schmidt, M.
Funding support Germany, 2items
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.
History
DepositionJun 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / 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_PubMed / _citation.title
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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
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
J: Serum amyloid A-2 protein
K: Serum amyloid A-2 protein
L: Serum amyloid A-2 protein


Theoretical massNumber of molelcules
Total (without water)112,34512
Polymers112,34512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area60940 Å2
ΔGint-188 kcal/mol
Surface area28080 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 12 / Rise per n subunits: 2.41 Å / Rotation per n subunits: 179.44 °)

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Components

#1: Protein
Serum amyloid A-2 protein


Mass: 9362.094 Da / Num. of mol.: 12 / 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: AA amyloid fibril / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Organ: spleen
Buffer solutionpH: 7
Buffer componentFormula: ddH2O
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20 mA, 0.25 mBar / Grid material: COPPER / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K

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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 FIELD / Nominal magnification: 105000 X / Nominal defocus max: -5500 nm / Nominal defocus min: -1300 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 20 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1063
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2SerialEM3.5image acquisition
4Gctf1.06CTF correction
7PHENIX1.12-2829model fitting
9PHENIX1.12-2829model refinement
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.44 ° / Axial rise/subunit: 2.41 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 137956
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21024 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL

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