+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8910 | |||||||||
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Title | Cryo-EM structure of murine AA amyloid fibril | |||||||||
Map data | Cryo-EM reconstruction of murine Serum Amyloid A fibrils from diseased mouse spleen using Relion 2.1. The central 30% of the reconstruction is shown. | |||||||||
Sample |
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Keywords | AA-amyloidosis / fibril / cross-beta / helical / 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 Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Liberta F / Fandrich M / Schmidt M | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8910.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-8910-v30.xml emd-8910.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8910_fsc.xml | 7.5 KB | Display | FSC data file |
Images | emd_8910.png | 273.8 KB | ||
Masks | emd_8910_msk_1.map | 35.3 MB | Mask map | |
Filedesc metadata | emd-8910.cif.gz | 5.6 KB | ||
Others | emd_8910_half_map_1.map.gz emd_8910_half_map_2.map.gz | 27.2 MB 27.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8910 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8910 | HTTPS FTP |
-Validation report
Summary document | emd_8910_validation.pdf.gz | 739 KB | Display | EMDB validaton report |
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Full document | emd_8910_full_validation.pdf.gz | 738.6 KB | Display | |
Data in XML | emd_8910_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_8910_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8910 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8910 | HTTPS FTP |
-Related structure data
Related structure data | 6dsoMC 9232C 6mstC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10825 (Title: Cryo electron microscopy of ex-vivo murine SAA amyloid fibrils Data size: 533.9 Data #1: Unaligned multiframe micrographs of ex-vivo murine SAA1 [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8910.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of murine Serum Amyloid A fibrils from diseased mouse spleen using Relion 2.1. The central 30% of the reconstruction is shown. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_8910_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Map 2 of two independently refined half maps
File | emd_8910_half_map_1.map | ||||||||||||
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Annotation | Map 2 of two independently refined half maps | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Map 1 of two independently refined half maps
File | emd_8910_half_map_2.map | ||||||||||||
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Annotation | Map 1 of two independently refined half maps | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AA amyloid fibril
Entire | Name: AA amyloid fibril |
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Components |
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-Supramolecule #1: AA amyloid fibril
Supramolecule | Name: AA amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) / Organ: spleen |
-Macromolecule #1: Serum amyloid A-2 protein
Macromolecule | Name: Serum amyloid A-2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 9.362094 KDa |
Sequence | String: GFFSFIGEAF QGAGDMWRAY TDMKEAGWKD GDKYFHARGN YDAAQRGPGG VWAAEKISDA RESFQEFFGR GHEDTMADQE ANR UniProtKB: Serum amyloid A-2 protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7 / Component - Formula: ddH2O |
Grid | Model: C-flat-2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER / Details: 20 mA, 0.25 mBar |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1063 / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -5.5 µm / Nominal defocus min: -1.3 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-6dso: |