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- PDB-8oq4: AApoAII amyloid fibril Morphology II (ex vivo) -

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Basic information

Entry
Database: PDB / ID: 8oq4
TitleAApoAII amyloid fibril Morphology II (ex vivo)
ComponentsApolipoprotein A-II
KeywordsPROTEIN FIBRIL / amyloid / systemic amyloidosis / misfolding disease / helical
Function / homology
Function and homology information


triglyceride-rich lipoprotein particle remodeling / lipase inhibitor activity / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / high-density lipoprotein particle binding / apolipoprotein receptor binding / lipoprotein metabolic process / chylomicron / phosphatidylcholine binding / high-density lipoprotein particle remodeling ...triglyceride-rich lipoprotein particle remodeling / lipase inhibitor activity / high-density lipoprotein particle receptor binding / spherical high-density lipoprotein particle / high-density lipoprotein particle binding / apolipoprotein receptor binding / lipoprotein metabolic process / chylomicron / phosphatidylcholine binding / high-density lipoprotein particle remodeling / very-low-density lipoprotein particle / high-density lipoprotein particle assembly / cholesterol transport / low-density lipoprotein particle remodeling / cholesterol binding / cholesterol metabolic process / cholesterol homeostasis / blood microparticle
Similarity search - Function
Apolipoprotein A-II (ApoA-II) / Apolipoprotein A-II (ApoA-II) superfamily / Apolipoprotein A-II (ApoA-II)
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsAndreotti, G. / Schmidt, M. / Faendrich, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)FA 456/27-1 Germany
German Research Foundation (DFG)FA 456/28-1 Germany
CitationJournal: J Mol Biol / Year: 2024
Title: Insights into the Structural Basis of Amyloid Resistance Provided by Cryo-EM Structures of AApoAII Amyloid Fibrils.
Authors: Giada Andreotti / Julian Baur / Marijana Ugrina / Peter Benedikt Pfeiffer / Max Hartmann / Sebastian Wiese / Hiroki Miyahara / Keiichi Higuchi / Nadine Schwierz / Matthias Schmidt / Marcus Fändrich /
Abstract: Amyloid resistance is the inability or the reduced susceptibility of an organism to develop amyloidosis. In this study we have analysed the molecular basis of the resistance to systemic AApoAII ...Amyloid resistance is the inability or the reduced susceptibility of an organism to develop amyloidosis. In this study we have analysed the molecular basis of the resistance to systemic AApoAII amyloidosis, which arises from the formation of amyloid fibrils from apolipoprotein A-II (ApoA-II). The disease affects humans and animals, including SAMR1C mice that express the C allele of ApoA-II protein, whereas other mouse strains are resistant to development of amyloidosis due to the expression of other ApoA-II alleles, such as ApoA-IIF. Using cryo-electron microscopy, molecular dynamics simulations and other methods, we have determined the structures of pathogenic AApoAII amyloid fibrils from SAMR1C mice and analysed the structural effects of ApoA-IIF-specific mutational changes. Our data show that these changes render ApoA-IIF incompatible with the specific fibril morphologies, with which ApoA-II protein can become pathogenic in vivo.
History
DepositionApr 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein A-II
B: Apolipoprotein A-II
C: Apolipoprotein A-II
D: Apolipoprotein A-II
E: Apolipoprotein A-II
F: Apolipoprotein A-II
G: Apolipoprotein A-II
H: Apolipoprotein A-II
I: Apolipoprotein A-II
L: Apolipoprotein A-II
M: Apolipoprotein A-II
N: Apolipoprotein A-II
O: Apolipoprotein A-II
P: Apolipoprotein A-II
Q: Apolipoprotein A-II
R: Apolipoprotein A-II
S: Apolipoprotein A-II
T: Apolipoprotein A-II
U: Apolipoprotein A-II
V: Apolipoprotein A-II
Z: Apolipoprotein A-II
W: Apolipoprotein A-II
J: Apolipoprotein A-II
K: Apolipoprotein A-II


Theoretical massNumber of molelcules
Total (without water)209,92124
Polymers209,92124
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area131580 Å2
ΔGint-469 kcal/mol
Surface area49930 Å2

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Components

#1: Protein ...
Apolipoprotein A-II


Mass: 8746.728 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: liver / Strain: SAMR1C / References: UniProt: A7YL62

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: AApoAII amyloid fibril / Type: COMPLEX
Details: AApoAII amyloid fibrils extracted from SAMR1C mice.
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Strain: SAMR1C / Organ: liver
Buffer solutionpH: 7 / Details: Water
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 294.15 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: SPOT SCAN
Electron lensMode: OTHER / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 12 sec. / Electron 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
1RELION3.1.2particle selection
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
12RELION3.1.23D reconstruction
19Coot0.9.5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.71 ° / Axial rise/subunit: 2.38 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 28656
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26946 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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