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The 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).

by helical reconstruction, at 10.1 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.4, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.4, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 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).
MapCross-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.
SampleHuman Abeta (1-40)
KeywordsAlzheimer's disease, micromechanical properties, electron cryo-microscopy, amyloid fibrils
AuthorsSachse C, Faendrich M, Grigorieff N
DateDeposition: 2009-10-10, Header release: 2009-10-12, Map release: 2009-10-12, Last update: 2011-01-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.4, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.4, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleAngew. Chem. Int. Ed. Engl., Vol. 49, Issue 7, Page 1321-3, Year 2010
TitleNanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy.
AuthorsCarsten Sachse, Nikolaus Grigorieff, Marcus Fändrich
MRC Laboratory of Molecular Biology, Cambridge, UK.
KeywordsAlzheimer Disease (metabolism), Amyloid (chemistry), Cryoelectron Microscopy, Humans, Nanotechnology, Protein Folding
LinksDOI: 10.1002/anie.200904781, PubMed: 20069616, PMC: PMC2913414
Map
Fileemd_5132.map.gz ( map file in CCP4 format, 314 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:1.4 (by author), 1.4 (movie #1):
Minimum - Maximum: -1.45155 - 3.52435
Average (Standard dev.): 1.26477e-08 (0.999994)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions4010020
Origin000
Limit399919
Spacing4010020
Unit CellA: 96 A, B: 240 A, C: 48 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.4 A
CCP4 map header info
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-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS1004020
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.4523.5240.000
Annotation DetailsCross-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.
Supplement
Images
Images
Sample
NameHuman Abeta (1-40)
Number of Components1
Oligomeric Statehelical
Theoretical Mass0.00433MDa
Component #1: protein - Abeta
Scientific nameAbeta
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionNo
Experiment
Sample Preparation
Helical ParametersAxial Symmetry: s2
Delta Z: 4.8 A
Hand: LEFT HANDED
StainingBlot for 7 seconds before plunging
Specimen Conc1 mg/ml
Specimen Support DetailsQuantifoil 400 mesh 1.3 micrometer holes
Specimen Statefilament
BufferpH: 8.7
Details: 50 mM Borate
Vitrification
MethodBlot for 7 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: custom-built plunging apparatus. in coldroom at 277 K.
InstrumentHOMEMADE PLUNGER
Temperature77.2 Kelvin
Imaging
MicroscopeFEI TECNAI F30
Date09-Nov-2005
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose35 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 59000, Calibrated: 58333
Astigmatismobjective lens astigmatism was corrected at 200,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1900 nm - 3500 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder
ModelGATAN LIQUID NITROGEN
Temperature93 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images62
Sampling Size7
Processing
Methodhelical reconstruction
3D reconstruction
Algorithmiterative algebraic reconstruction
Euler Angles Detailsone-degree sampling around helical axis, out-of-plane tilt 16 degree deviation (in 1 degree steps)
SoftwareSPIDER
CTF CorrectionEach particle CTFTILT
Resolution By Author10.1 A
Resolution Method10.1
Helical
DetailsThe 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.
Download
Data from EMDB
Header (meta data in XML format)emd-5132.xml (7.8 KB)
Map dataemd_5132.map.gz (285.4 KB)
Imagesemd_5132_1.tif (54.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5132
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 3.7 MB
Session file for UCSF-Chimera, 26.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.5 MB
Session file for UCSF-Chimera, 26.2 KB