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- EMDB-17104: AApoAII amyloid fibril Morphology II (ex vivo) -

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Basic information

Entry
Database: EMDB / ID: EMD-17104
TitleAApoAII amyloid fibril Morphology II (ex vivo)
Map dataAApoAII fibril density map
Sample
  • Complex: AApoAII amyloid fibril
    • Protein or peptide: Apolipoprotein A-II
Keywordsamyloid / protein fibril / systemic amyloidosis / misfolding disease / helical
Function / homologyApolipoprotein A-II (ApoA-II) / Apolipoprotein A-II (ApoA-II) superfamily / Apolipoprotein A-II (ApoA-II) / lipoprotein metabolic process / high-density lipoprotein particle / lipid transport / lipid binding / Apolipoprotein A-II
Function and homology information
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsAndreotti G / Schmidt M / Faendrich M
Funding support Germany, 2 items
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, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17104.png

Downloads & links

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Map

FileDownload / File: emd_17104.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAApoAII fibril density map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00853
Minimum - Maximum-0.020960873 - 0.049297713
Average (Standard dev.)0.000043093016 (±0.0009962575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17104_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Extended AApoAII fibril density map

Fileemd_17104_additional_1.map
AnnotationExtended AApoAII fibril density map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_17104_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_17104_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AApoAII amyloid fibril

EntireName: AApoAII amyloid fibril
Components
  • Complex: AApoAII amyloid fibril
    • Protein or peptide: Apolipoprotein A-II

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Supramolecule #1: AApoAII amyloid fibril

SupramoleculeName: AApoAII amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: AApoAII amyloid fibrils extracted from SAMR1C mice.
Source (natural)Organism: Mus musculus (house mouse) / Strain: SAMR1C / Organ: liver

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Macromolecule #1: Apolipoprotein A-II

MacromoleculeName: Apolipoprotein A-II / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: SAMR1C / Organ: liver
Molecular weightTheoretical: 8.746728 KDa
SequenceString:
QADGQDMQSL FTQYFQSMTE YGKDLVEKAK TSEIQSQAKA YFEKTHEQLT PLVRSAGTSL VNFFSSLMNL EEKPAPAA

UniProtKB: Apolipoprotein A-II

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7 / Details: Water
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 294.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 12.0 sec. / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.38 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.71 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 26946
Segment selectionNumber selected: 28656 / Software - Name: RELION (ver. 3.1.2)
Startup modelType of model: NONE / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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