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- EMDB-8910: Cryo-EM structure of murine AA amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-8910
TitleCryo-EM structure of murine AA amyloid fibril
Map dataCryo-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
  • Complex: AA amyloid fibril
    • Protein or peptide: Serum amyloid A-2 protein
KeywordsAA-amyloidosis / fibril / cross-beta / helical / PROTEIN FIBRIL
Function / homology
Function and homology information


response to stilbenoid / high-density lipoprotein particle / cytoplasmic microtubule / G protein-coupled receptor binding / acute-phase response
Similarity search - Function
Serum amyloid A protein / Serum amyloid A protein / Serum amyloid A proteins signature. / Serum amyloid A proteins
Similarity search - Domain/homology
Serum amyloid A-2 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiberta F / Fandrich M / Schmidt M
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG FA 456/15-1 Germany
German Research Foundation (DFG)DFG SCHM 3276/1 Germany
CitationJournal: 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
DepositionJun 14, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseMar 13, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6dso
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6dso
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8910.png

Downloads & links

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Map

FileDownload / File: emd_8910.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-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

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 210 pix.
= 283.5 Å		1.35 Å/pix.
x 210 pix.
= 283.5 Å		1.35 Å/pix.
x 210 pix.
= 283.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.17764086 - 0.34451205
Average (Standard dev.)0.0008869683 (±0.010962577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 283.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z210210210
origin x/y/z0.0000.0000.000
length x/y/z283.500283.500283.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.1780.3450.001

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Supplemental data

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Mask #1

Fileemd_8910_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Map 2 of two independently refined half maps

Fileemd_8910_half_map_1.map
AnnotationMap 2 of two independently refined half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Map 1 of two independently refined half maps

Fileemd_8910_half_map_2.map
AnnotationMap 1 of two independently refined half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AA amyloid fibril

EntireName: AA amyloid fibril
Components
  • Complex: AA amyloid fibril
    • Protein or peptide: Serum amyloid A-2 protein

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Supramolecule #1: AA amyloid fibril

SupramoleculeName: AA amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse) / Organ: spleen

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Macromolecule #1: Serum amyloid A-2 protein

MacromoleculeName: Serum amyloid A-2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.362094 KDa
SequenceString:
GFFSFIGEAF QGAGDMWRAY TDMKEAGWKD GDKYFHARGN YDAAQRGPGG VWAAEKISDA RESFQEFFGR GHEDTMADQE ANR

UniProtKB: Serum amyloid A-2 protein

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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

Concentration0.2 mg/mL
BufferpH: 7 / Component - Formula: ddH2O
GridModel: C-flat-2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER / Details: 20 mA, 0.25 mBar
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -5.5 µm / Nominal defocus min: -1.3 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1063 / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 137956 / Software - Name: RELION (ver. 2.1)
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 2.41 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.44 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 21024
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6dso:
Cryo-EM structure of murine AA amyloid fibril

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