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- EMDB-5132: The reconstructed F120 amyloid fibril represents the structure of... -

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Basic information

Entry
Database: EMDB / ID: 5132
TitleThe reconstructed F120 amyloid fibril represents the structure of a selected subpopulation from the Abeta(1-40) fibril sample with a mean crossover distance of 120 nm. The F140 subpopulation with a mean crossover distance of 140 nm had been studied and deposited previously (EMDB accession no. 5008).
KeywordsAlzheimer's disease / micromechanical properties / electron cryo-microscopy / amyloid fibrils
SampleHuman Abeta (1-40)
SourceHomo sapiens / human
Map dataCross-sectional density slice of the F120 amyloid fibril of 24 Angstrom thickness. F120 corresponds to a subpopulation of the Abeta(1-40) amyloid fibril sample with a mean crossover distance of 120 nm.
Methodhelical reconstruction, at 10.1 A resolution
AuthorsSachse C / Faendrich M / Grigorieff N
CitationAngew. Chem. Int. Ed. Engl., 2010, 49, 1321-1323

Angew. Chem. Int. Ed. Engl., 2010, 49, 1321-1323 StrPapers
Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy.
Carsten Sachse / Nikolaus Grigorieff / Marcus Fändrich

DateDeposition: Oct 10, 2009 / Header (metadata) release: Oct 12, 2009 / Map release: Oct 12, 2009 / Last update: Oct 10, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.4
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 1.4
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_5132.map.gz (map file in CCP4 format, 314 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
20 pix
2.4 A/pix
= 48. A
40 pix
2.4 A/pix
= 240. A
100 pix
2.4 A/pix
= 96. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.4 A
Density
Contour Level:1.4 (by author), 1.4 (movie #1):
Minimum - Maximum-1.45155275 - 3.52434707
Average (Standard dev.)1E-8 (0.9999938)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions4010020
Origin000
Limit399919
Spacing1004020
CellA: 96 A / B: 240.00002 A / C: 48 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.42.42.4
M x/y/z4010020
origin x/y/z0.0000.0000.000
length x/y/z96.000240.00048.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS1004020
D min/max/mean-1.4523.5240.000

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Supplemental data

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Sample components

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Entire Human Abeta (1-40)

EntireName: Human Abeta (1-40) / Number of components: 1 / Oligomeric State: helical
MassTheoretical: 4.33 kDa

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Component #1: protein, Abeta

ProteinName: Abeta / a.k.a: Abeta / Recombinant expression: No
SourceSpecies: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C2 (2 fold cyclic) / Hand: LEFT HANDED / Delta z: 4.8 A
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 50 mM Borate / pH: 8.7
Support filmQuantifoil 400 mesh 1.3 micrometer holes
StainingBlot for 7 seconds before plunging
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77.2 K / Method: Blot for 7 seconds before plunging
Details: Vitrification instrument: custom-built plunging apparatus. in coldroom at 277 K.

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F30 / Date: Nov 9, 2005
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 58333 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1900 - 3500 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 93 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 62 / Scanner: ZEISS SCAI / Sampling size: 7 microns

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Image processing

ProcessingMethod: helical reconstruction
Details: The fibrils in the sample were selected based on their uniform width. 2. The F120 subset of limited crossover distances (110-130 nm) was chosen for the reconstruction.
3D reconstructionAlgorithm: iterative algebraic reconstruction
Euler angles: one-degree sampling around helical axis, out-of-plane tilt 16 degree deviation (in 1 degree steps)
Software: SPIDER / CTF correction: Each particle CTFTILT / Resolution: 10.1 A / Resolution method: 10.1

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