+Open data
-Basic information
Entry | Database: PDB / ID: 8oq4 | |||||||||
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Title | AApoAII amyloid fibril Morphology II (ex vivo) | |||||||||
Components | Apolipoprotein A-II | |||||||||
Keywords | PROTEIN 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 | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Andreotti, G. / Schmidt, M. / Faendrich, M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oq4.cif.gz | 276 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oq4.ent.gz | 220.7 KB | Display | PDB format |
PDBx/mmJSON format | 8oq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oq4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8oq4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8oq4_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 8oq4_validation.cif.gz | 72 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/8oq4 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/8oq4 | HTTPS FTP |
-Related structure data
Related structure data | 17104MC 8oq5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: AApoAII amyloid fibril / Type: COMPLEX Details: AApoAII amyloid fibrils extracted from SAMR1C mice. Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) / Strain: SAMR1C / Organ: liver |
Buffer solution | pH: 7 / Details: Water |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 294.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: 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 recording | Average exposure time: 12 sec. / Electron dose: 42.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 179.71 ° / Axial rise/subunit: 2.38 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 28656 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26946 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |