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- EMDB-9232: Cryo-EM structure of human AA amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-9232
TitleCryo-EM structure of human AA amyloid fibril
Map dataCryo-EM reconstruction of human Serum Amyloid A fibrils, extracted from diseased human kidney. The fibril shows a helical rise of 2.40 A, a helical twist of 180.79 degree and a resolution of 2.7 A.
Sample
  • Complex: human AA amyloid fibril
    • Protein or peptide: Serum amyloid A-1 protein
KeywordsAA-amyloidosis / Serum Amyloid A / cross-beta / helical / protein fibril
Function / homology
Function and homology information


Scavenging by Class B Receptors / lymphocyte chemotaxis / positive regulation of interleukin-1 production / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / macrophage chemotaxis / regulation of protein secretion / cytoplasmic microtubule / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling ...Scavenging by Class B Receptors / lymphocyte chemotaxis / positive regulation of interleukin-1 production / high-density lipoprotein particle / Formyl peptide receptors bind formyl peptides and many other ligands / macrophage chemotaxis / regulation of protein secretion / cytoplasmic microtubule / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / endocytic vesicle lumen / neutrophil chemotaxis / positive regulation of cell adhesion / positive regulation of cytokine production / acute-phase response / G protein-coupled receptor binding / TAK1-dependent IKK and NF-kappa-B activation / platelet activation / negative regulation of inflammatory response / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / Interleukin-4 and Interleukin-13 signaling / G alpha (q) signalling events / Amyloid fiber formation / extracellular exosome / extracellular region
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-1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsRennegarbe M / Liberta 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
Header (metadata) releaseAug 1, 2018-
DepositionOct 18, 2018-
Map releaseMar 13, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface view colored by cylindrical radius
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  • Surface view with fitted model
  • Atomic models: PDB-6mst
  • Surface level: 0.05
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mst
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Structure viewerEM map:
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Supplemental images

emd_9232.png

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Map

FileDownload / File: emd_9232.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of human Serum Amyloid A fibrils, extracted from diseased human kidney. The fibril shows a helical rise of 2.40 A, a helical twist of 180.79 degree and a resolution of 2.7 A.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 270 pix.
= 280.8 Å		1.04 Å/pix.
x 270 pix.
= 280.8 Å		1.04 Å/pix.
x 270 pix.
= 280.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.23911723 - 0.5025357
Average (Standard dev.)0.00038090933 (±0.009526984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 280.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z280.800280.800280.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.2390.5030.000

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Supplemental data

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Mask #1

Fileemd_9232_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the two independently refined half maps.

Fileemd_9232_half_map_1.map
AnnotationOne of the two independently refined half maps.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the two independently refined half maps.

Fileemd_9232_half_map_2.map
AnnotationOne of the 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 : human AA amyloid fibril

EntireName: human AA amyloid fibril
Components
  • Complex: human AA amyloid fibril
    • Protein or peptide: Serum amyloid A-1 protein

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Supramolecule #1: human AA amyloid fibril

SupramoleculeName: human AA amyloid fibril / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organ: kidney

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Macromolecule #1: Serum amyloid A-1 protein

MacromoleculeName: Serum amyloid A-1 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.481154 KDa
SequenceString:
SFFSFLGEAF DGARDMWRAY SDMREANYIG SDKYFHARGN YDAAKRGPGG VWAAEAISDA RENIQR

UniProtKB: Serum amyloid A-1 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-1.2/1.3 4C / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.025 kPa / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.79 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 91872
Segment selectionNumber selected: 93025 / Software - Name: RELION (ver. 2.1)
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6mst:
Cryo-EM structure of human AA amyloid fibril

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