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

by helical reconstruction, at 23 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.1, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.1, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1650
TitleReconstruction of a 13 nm wide Abeta(1-40) amyloid fibril
MapThis is a reconstruction of an Abeta(1-40) amyloid fibril
SampleAbeta(1-40) amyloid fibril
KeywordsAlzheimer's disease, amyloid, prion, protein folding
AuthorsSchmidt M, Sachse C, Richter W, Xu C, Fandrich M, Grigorieff N
DateDeposition: 2009-09-11, Header release: 2009-09-24, Map release: 2009-09-24, Last update: 2011-09-07
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.1, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.1, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 106, Issue 47, Page 19813-8, Year 2009
TitleComparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures.
AuthorsMatthias Schmidt, Carsten Sachse, Walter Richter, Chen Xu, Marcus Fändrich, Nikolaus Grigorieff
KeywordsAlzheimer Disease (pathology), Amyloid (chemistry), Amyloid beta-Peptides (chemistry), Cryoelectron Microscopy, Hydrogen-Ion Concentration, Image Processing, Computer-Assisted, Microscopy, Electron, Transmission (methods), Models, Molecular, Molecular Sequence Data, Peptide Fragments (chemistry), Protein Structure, Tertiary, Spectroscopy, Fourier Transform Infrared (methods), amyloid beta-protein (1-40), amyloid beta-protein (1-42)
LinksDOI: 10.1073/pnas.0905007106, PubMed: 19843697, PMC: PMC2764733
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.

Density
Contour Level:0.055 (by author), 0.1 (movie #1):
Minimum - Maximum: -0.313765 - 0.515397
Average (Standard dev.): 0.00522568 (0.124983)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions404010
Origin000
Limit39399
Spacing404010
Unit CellA: 192 A, B: 192 A, C: 48 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.8 A
CCP4 map header info
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-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404010
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.3140.5150.005
Annotation DetailsThis is a reconstruction of an Abeta(1-40) amyloid fibril
Supplement
Images
Images
Sample
NameAbeta(1-40) amyloid fibril
Number of Components1
Oligomeric StateCross-beta structure
Component #1: protein - Alzheimer peptide
Scientific nameAbeta(1-40) peptide
Common NameAlzheimer peptide
Theoretical Mass0.00433 MDa
Oligomeric DetailsCross-beta
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Experiment
Sample Preparation
Helical ParametersAxial Symmetry: s2
Hand: LEFT HANDED
Specimen Conc1 mg/ml
Specimen Support Details400 mesh copper grid
Specimen StatehelicalArray
Crystal Grow DetailsIncubation for 4 days at 4 degC
BufferpH: 8.7
Details: 50 mM sodium borate
Vitrification
MethodOne-sided blotting for 5 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Manual plunger (Brandeis)
Humidity30
InstrumentHOMEMADE PLUNGER
Temperature90 Kelvin
Imaging
MicroscopeFEI TECNAI F30
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose35 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 59000, Calibrated: 58090
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 3500 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature90 K ( 90 - 90 K)
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
Od Range1.2
ScannerZEISS SCAI
Number of Digital Images4
Sampling Size7
Quant Bit Number12
Processing
Methodhelical reconstruction
3D reconstruction
AlgorithmWeighted back projection
SoftwareSpider
CTF CorrectionEach particle
DetailsFinal map was calculated from 4 fibrils
Resolution By Author23 A
Resolution MethodFSC 0.5
Helical
DetailsFibrils were selected using BOXER
Download
Data from EMDB
Header (meta data in XML format)emd-1650.xml (7.4 KB)
Map dataemd_1650.map.gz (58.5 KB)
ImagesEMD-1650.tif (37.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1650
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 3.5 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 2.9 MB
Session file for UCSF-Chimera, 26.4 KB