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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 data
Samplehuman AA amyloid fibril:
Serum amyloid A-1 protein
Function / homology
Function and homology information


positive regulation of interleukin-1 secretion / lymphocyte chemotaxis / macrophage chemotaxis / high-density lipoprotein particle / regulation of protein secretion / cytoplasmic microtubule / positive regulation of cell adhesion / chemoattractant activity / endocytic vesicle lumen / G protein-coupled receptor binding ...positive regulation of interleukin-1 secretion / lymphocyte chemotaxis / macrophage chemotaxis / high-density lipoprotein particle / regulation of protein secretion / cytoplasmic microtubule / positive regulation of cell adhesion / chemoattractant activity / endocytic vesicle lumen / G protein-coupled receptor binding / positive regulation of cytokine secretion / cell chemotaxis / neutrophil chemotaxis / acute-phase response / negative regulation of inflammatory response / receptor-mediated endocytosis / positive regulation of cytosolic calcium ion concentration / platelet activation / heparin binding / activation of MAPK activity / G protein-coupled receptor signaling pathway / cytokine-mediated signaling pathway / cellular protein metabolic process / innate immune response / cell / extracellular space / extracellular exosome / extracellular region
Serum amyloid A protein
Serum amyloid A-1 protein
Biological speciesHomo sapiens (human) / Human (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.
Validation ReportPDB-ID: 6mst

SummaryFull reportAbout validation report
History
Header (metadata) releaseAug 1, 2018-
DepositionOct 18, 2018-
Map releaseMar 13, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6mst
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mst
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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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)
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
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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Segmentation: #1

Fileemd_9232_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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

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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

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Sample components

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Entire human AA amyloid fibril

EntireName: human AA amyloid fibril / Number of components: 2

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Component #1: protein, human AA amyloid fibril

ProteinName: human AA amyloid fibril / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (natural)Organ or tissue: kidney

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Component #2: protein, Serum amyloid A-1 protein

ProteinName: Serum amyloid A-1 protein / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 7.481154 kDa
SourceSpecies: Human (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 2.4 Å / Delta phi: 0.79 %deg;
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 7
Support film15 mA
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -500.0 - -2500.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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