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Reconstruction of a 13 nm wide Abeta(1-40) amyloid fibril
by helical reconstruction, at 23 A resolution
#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 / ID | EM DATA BANK (EMDB) / 1650 |
|---|---|
| Authors | Schmidt M, Sachse C, Richter W, Xu C, Fandrich M, Grigorieff N |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie 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 viewers |  Yorodumi,  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 | |
| Article | Proc. Natl. Acad. Sci. U.S.A., Vol. 106, Issue 47, Page 19813-8, Year 2009 |
|---|---|
| Title | Comparison of Alzheimer Abeta(1-40) and Abeta(1-42) amyloid fibrils reveals similar protofilament structures. |
| Authors | Matthias 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. |
| Keywords |  Alzheimer 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) |
| Links | DOI: 10.1073/pnas.0905007106, PubMed: 19843697, PMC: PMC2764733 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1650.map ( map file in CCP4 format, 66 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 192 A , B = 192 A , C = 48 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 4.8 A , Y = 4.8 A , Z = 4.8 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a reconstruction of an Abeta(1-40) amyloid fibril | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Abeta(1-40) amyloid fibril |
|---|---|
| Number of Components | 1 |
| Oligomeric State | Cross-beta structure |
| Component #1: protein - Alzheimer peptide | |
| Scientific name | Abeta(1-40) peptide |
| Common Name | Alzheimer peptide |
| Theoretical Mass | 0.00433 MDa |
| Oligomeric Details | Cross-beta |
| Scientific Name of Species | Homo sapiens (NCBI Taxonomy: 9606) |
| Common Name of Species | Human |
| Recombinant expression | Yes |
 Experiment | |
| Sample Preparation | |
| Helical Parameters | Axial Symmetry: s2 Hand: LEFT HANDED |
|---|---|
| Specimen Conc | 1 mg/ml |
| Specimen Support Details | 400 mesh copper grid |
| Specimen State | helicalArray |
| Crystal Grow Details | Incubation for 4 days at 4 degC |
| Buffer | pH: 8.7 Details: 50 mM sodium borate |
| Vitrification | |
| Method | One-sided blotting for 5 seconds before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Manual plunger (Brandeis) |
| Humidity | 30 |
| Instrument | HOMEMADE PLUNGER |
| Temperature | 90 Kelvin |
| Imaging | |
| Microscope | FEI TECNAI F30 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 35 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 59000 X, Calibrated: 58090 X |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 2000 nm - 3500 nm |
| Specimen Holder | |
| Holder | Eucentric ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | 90 Kelvin ( 90 Kelvin - 90 Kelvin ) |
| Camera | |
| Detector | Kodak SO 163 film |
| Image Acquisition | |
| Od Range | 1.2 |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 4 |
| Sampling Size | 7 microns |
| Quant Bit Number | 12 |
 Processing | |
| Method | helical reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Weighted back projection |
| Software | Spider |
| CTF Correction | Each particle |
| Details | Final map was calculated from 4 fibrils |
| Resolution By Author | 23 |
| Resolution Method | FSC at 0.5 cut-off |
| Helical | |
| Details | Fibrils were selected using BOXER |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1650.xml (7.4 KB) | ||
|---|---|---|---|
| Map data | emd_1650.map.gz (58.5 KB) | ||
| Images | EMD-1650.tif (37.8 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1650 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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