3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-5132

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-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
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
#1
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