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- EMDB-14726: Cryo-EM structure of ex vivo AA amyloid from renal tissue of a sh... -

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Entry
Database: EMDB / ID: EMD-14726
TitleCryo-EM structure of ex vivo AA amyloid from renal tissue of a short hair cat deceased in a shelter
Map dataautosharpened map
Sample
  • Organelle or cellular component: AA amyloid extracted from kidney of deceased cat
    • Protein or peptide: Serum amyloid A proteinSerum amyloid A
Function / homologySerum 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 speciesFelis catus (domestic cat) / domestic cat (domestic cat)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSchulte T / Chaves-Sanjuan A / Ricagno S
Funding support Italy, 1 items
OrganizationGrant numberCountry
Italian Ministry of Health Italy
CitationJournal: 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
DepositionApr 5, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14726.png

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Map

FileDownload / File: emd_14726.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationautosharpened map
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
0.89 Å/pix.
x 250 pix.
= 222.25 Å		0.89 Å/pix.
x 250 pix.
= 222.25 Å		0.89 Å/pix.
x 250 pix.
= 222.25 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-13.81175 - 15.306102
Average (Standard dev.)3.7594588e-13 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 222.25 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14726_msk_1.map
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AxesZYX

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Additional map: map after 3D autorefine with gold-standard solvent-flattened fsc

Fileemd_14726_additional_1.map
Annotationmap after 3D autorefine with gold-standard solvent-flattened fsc
Projections & Slices
AxesZYX

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Histogram

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Half map: half map 2

Fileemd_14726_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Histogram

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Half map: half map 1

Fileemd_14726_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Sample components

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Entire : AA amyloid extracted from kidney of deceased cat

EntireName: AA amyloid extracted from kidney of deceased cat
Components
  • Organelle or cellular component: AA amyloid extracted from kidney of deceased cat
    • Protein or peptide: Serum amyloid A proteinSerum amyloid A

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Supramolecule #1: AA amyloid extracted from kidney of deceased cat

SupramoleculeName: AA amyloid extracted from kidney of deceased cat / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Felis catus (domestic cat) / Organ: kidney

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Macromolecule #1: Serum amyloid A protein

MacromoleculeName: Serum amyloid A protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: domestic cat (domestic cat)
Molecular weightTheoretical: 14.449766 KDa
SequenceString:
MKLFTGLVFC SLVLGVSSEW YSFLGEAAQG AWDMWRAYSD MREANYIGAD KYFHARGNYD AAQRGPGGAW AAKVISDARE NSQRVTDFF RHGNSGHGAE DSKADQEANE WGRSGKDPNH YRPEGLPDKY

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
Details: glow discharged for 30s at 30mA using a GloQube system
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.9043 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.29627 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 65000
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 76.7
Output model

PDB-7zh7:
Cryo-EM structure of ex vivo AA amyloid from renal tissue of a short hair cat deceased in a shelter

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