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- EMDB-1650: Reconstruction of a 13 nm wide Abeta(1-40) amyloid fibril -

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Basic information

Entry
Database: EMDB / ID: 1650
TitleReconstruction of a 13 nm wide Abeta(1-40) amyloid fibril
KeywordsAlzheimer's disease / amyloid / prion / protein folding
SampleAbeta(1-40) amyloid fibril
SourceHomo sapiens / human
Map dataThis is a reconstruction of an Abeta(1-40) amyloid fibril
Methodhelical reconstruction, at 23 A resolution
AuthorsSchmidt M / Sachse C / Richter W / Xu C / Fandrich M / Grigorieff N
CitationProc. Natl. Acad. Sci. U.S.A., 2009, 106, 19813-19818

Proc. Natl. Acad. Sci. U.S.A., 2009, 106, 19813-19818 StrPapers
Comparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures.
Matthias Schmidt / Carsten Sachse / Walter Richter / Chen Xu / Marcus Fändrich / Nikolaus Grigorieff

DateDeposition: Sep 11, 2009 / Header (metadata) release: Sep 24, 2009 / Map release: Sep 24, 2009 / Last update: Sep 11, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1650.map.gz (map file in CCP4 format, 64 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
10 pix
4.8 A/pix
= 48. A
40 pix
4.8 A/pix
= 192. A
40 pix
4.8 A/pix
= 192. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.8 A
Density
Contour Level:0.055 (by author), 0.1 (movie #1):
Minimum - Maximum-0.313765 - 0.515397
Average (Standard dev.)0.00522568 (0.124983)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions404010
Origin000
Limit39399
Spacing404010
CellA: 192 A / B: 192 A / C: 48 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z4.84.84.8
M x/y/z404010
origin x/y/z0.0000.0000.000
length x/y/z192.000192.00048.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404010
D min/max/mean-0.3140.5150.005

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Supplemental data

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Sample components

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Entire Abeta(1-40) amyloid fibril

EntireName: Abeta(1-40) amyloid fibril / Number of components: 1 / Oligomeric State: Cross-beta structure

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Component #1: protein, Abeta(1-40) peptide

ProteinName: Abeta(1-40) peptide / a.k.a: Alzheimer peptide / Oligomeric Details: Cross-beta / Recombinant expression: Yes
MassTheoretical: 4.33 kDa
SourceSpecies: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen statehelical array
Helical parametersAxial symmetry: C2 (2 fold cyclic) / Hand: LEFT HANDED
Crystal grow detailsIncubation for 4 days at 4 degC
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 50 mM sodium borate / pH: 8.7
Support film400 mesh copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 30 % / Method: One-sided blotting for 5 seconds before plunging
Details: Vitrification instrument: Manual plunger (Brandeis)

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 58090 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 3500 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 90 K ( 90 - 90 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 4 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1.2

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Image processing

ProcessingMethod: helical reconstruction / Details: Fibrils were selected using BOXER
3D reconstructionAlgorithm: Weighted back projection / Software: Spider / CTF correction: Each particle / Details: Final map was calculated from 4 fibrils / Resolution: 23 A / Resolution method: FSC 0.5

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