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- EMDB-11163: Amyloid fibril morphology ii (in vitro) from murine SAA1.1 protein -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11163 | |||||||||||||||||||||
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Title | Amyloid fibril morphology ii (in vitro) from murine SAA1.1 protein | |||||||||||||||||||||
![]() | in vitro mSAA amyloid fibril morphology ii | |||||||||||||||||||||
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![]() | systemic amyloidosis / misfolding disease / inflammation / prion / PROTEIN FIBRIL | |||||||||||||||||||||
Function / homology | Serum 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![]() | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.95 Å | |||||||||||||||||||||
![]() | Bansal A / Schmidt M | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
Images | ![]() | 83.8 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 22.4 MB 22.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 797.3 KB | Display | ![]() |
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Full document | ![]() | 796.9 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zcgMC ![]() 6zcfC ![]() 6zchC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 525.4 Data #1: Unaligned multiframe micrographs of ex-vivo murine SAA1 [micrographs - multiframe] Data #2: Thumbnails for micrographs of ex-vivo murine SAA1 [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | in vitro mSAA amyloid fibril morphology ii | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: in vitro mSAA amyloid fibril morphology ii half map 2
File | emd_11163_half_map_1.map | ||||||||||||
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Annotation | in vitro mSAA amyloid fibril morphology ii half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: in vitro mSAA amyloid fibril morphology ii half map 1
File | emd_11163_half_map_2.map | ||||||||||||
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Annotation | in vitro mSAA amyloid fibril morphology ii half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Serum amyloid A1 (SAA1) amyloid fibril
Entire | Name: Serum amyloid A1 (SAA1) amyloid fibril |
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Components |
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-Supramolecule #1: Serum amyloid A1 (SAA1) amyloid fibril
Supramolecule | Name: Serum amyloid A1 (SAA1) amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: in vitro murine SAA amyloid fibril morphology ii |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Serum amyloid A-2 protein
Macromolecule | Name: Serum amyloid A-2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.622629 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GFFSFIGEAF QGAGDMWRAY TDMKEAGWKD GDKYFHARGN YDAAQRGPGG VWAAEKISDA RESFQEFFGR GHEDTMADQE ANRHGRSGK DPNYYRPPGL PAKY UniProtKB: Serum amyloid A-2 protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8.5 / Component - Concentration: 10.0 mM / Component - Formula: (HOCH2)3CNH2 / Component - Name: Tris(hydroxymethyl)aminomethane / Details: 10mM Tris(hydroxymethyl)aminomethane (Tris) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 96 % / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 12.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.74874 Å Applied symmetry - Helical parameters - Δ&Phi: -1.6 ° Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 21355 |
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Segment selection | Number selected: 80724 |
Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE / Target criteria: Correlation coefficient |
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Output model | ![]() PDB-6zcg: |