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Yorodumi- EMDB-14726: Cryo-EM structure of ex vivo AA amyloid from renal tissue of a sh... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14726 | |||||||||
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Title | Cryo-EM structure of ex vivo AA amyloid from renal tissue of a short hair cat deceased in a shelter | |||||||||
Map data | autosharpened map | |||||||||
Sample |
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Keywords | AA amyloidosis / cat / Serum amyloid A / PROTEIN FIBRIL | |||||||||
Function / homology | Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins / high-density lipoprotein particle / acute-phase response / Serum amyloid A protein Function and homology information | |||||||||
Biological species | Felis catus (domestic cat) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Schulte T / Chaves-Sanjuan A / Ricagno S | |||||||||
Funding support | Italy, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structure of ex vivo fibrils associated with extreme AA amyloidosis prevalence in a cat shelter. Authors: Tim Schulte / Antonio Chaves-Sanjuan / Giulia Mazzini / Valentina Speranzini / Francesca Lavatelli / Filippo Ferri / Carlo Palizzotto / Maria Mazza / Paolo Milani / Mario Nuvolone / Anne- ...Authors: Tim Schulte / Antonio Chaves-Sanjuan / Giulia Mazzini / Valentina Speranzini / Francesca Lavatelli / Filippo Ferri / Carlo Palizzotto / Maria Mazza / Paolo Milani / Mario Nuvolone / Anne-Cathrine Vogt / Monique Vogel / Giovanni Palladini / Giampaolo Merlini / Martino Bolognesi / Silvia Ferro / Eric Zini / Stefano Ricagno / Abstract: AA amyloidosis is a systemic disease characterized by deposition of misfolded serum amyloid A protein (SAA) into cross-β amyloid in multiple organs in humans and animals. AA amyloidosis occurs at ...AA amyloidosis is a systemic disease characterized by deposition of misfolded serum amyloid A protein (SAA) into cross-β amyloid in multiple organs in humans and animals. AA amyloidosis occurs at high SAA serum levels during chronic inflammation. Prion-like transmission was reported as possible cause of extreme AA amyloidosis prevalence in captive animals, e.g. 70% in cheetah and 57-73% in domestic short hair (DSH) cats kept in zoos and shelters, respectively. Herein, we present the 3.3 Å cryo-EM structure of AA amyloid extracted post-mortem from the kidney of a DSH cat with renal failure, deceased in a shelter with extreme disease prevalence. The structure reveals a cross-β architecture assembled from two 76-residue long proto-filaments. Despite >70% sequence homology to mouse and human SAA, the cat SAA variant adopts a distinct amyloid fold. Inclusion of an eight-residue insert unique to feline SAA contributes to increased amyloid stability. The presented feline AA amyloid structure is fully compatible with the 99% identical amino acid sequence of amyloid fragments of captive cheetah. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14726.map.gz | 53.8 MB | EMDB map data format | |
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Header (meta data) | emd-14726-v30.xml emd-14726.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14726_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_14726.png | 135.6 KB | ||
Masks | emd_14726_msk_1.map | 59.6 MB | Mask map | |
Filedesc metadata | emd-14726.cif.gz | 5.6 KB | ||
Others | emd_14726_additional_1.map.gz emd_14726_half_map_1.map.gz emd_14726_half_map_2.map.gz | 44.1 MB 44.5 MB 44.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14726 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14726 | HTTPS FTP |
-Validation report
Summary document | emd_14726_validation.pdf.gz | 916.2 KB | Display | EMDB validaton report |
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Full document | emd_14726_full_validation.pdf.gz | 915.7 KB | Display | |
Data in XML | emd_14726_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | emd_14726_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14726 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14726 | HTTPS FTP |
-Related structure data
Related structure data | 7zh7MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14726.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | autosharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.889 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14726_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: map after 3D autorefine with gold-standard solvent-flattened fsc
File | emd_14726_additional_1.map | ||||||||||||
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Annotation | map after 3D autorefine with gold-standard solvent-flattened fsc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_14726_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_14726_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : AA amyloid extracted from kidney of deceased cat
Entire | Name: AA amyloid extracted from kidney of deceased cat |
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Components |
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-Supramolecule #1: AA amyloid extracted from kidney of deceased cat
Supramolecule | Name: AA amyloid extracted from kidney of deceased cat / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Felis catus (domestic cat) / Organ: kidney |
-Macromolecule #1: Serum amyloid A protein
Macromolecule | Name: Serum amyloid A protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Felis catus (domestic cat) |
Molecular weight | Theoretical: 14.449766 KDa |
Sequence | String: MKLFTGLVFC SLVLGVSSEW YSFLGEAAQG AWDMWRAYSD MREANYIGAD KYFHARGNYD AAQRGPGGAW AAKVISDARE NSQRVTDFF RHGNSGHGAE DSKADQEANE WGRSGKDPNH YRPEGLPDKY UniProtKB: Serum amyloid A protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. Details: glow discharged for 30s at 30mA using a GloQube system |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2652 / Average electron dose: 40.0 e/Å2 / Details: images takes for analysis |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 120000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 76.7 |
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Output model | PDB-7zh7: |