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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, Made by UCSF CHIMERA

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

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

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
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
Rosenstiel Basic Medical Sciences Research Center and Howard Hughes Medical Institute, Brandeis University, MS 029, Waltham, MA 02454-9110, USA.
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
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