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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
#1: Surface view with section colored by density value, Surface level: 1.4, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 1.4, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5132 |
|---|---|
| Authors | Sachse C, Faendrich 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: 1.4, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 1.4, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  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 | |
| Article | Angew. Chem. Int. Ed. Engl., Vol. 49, Issue 7, Page 1321-3, Year 2010 |
|---|---|
| Title | Nanoscale flexibility parameters of Alzheimer amyloid fibrils determined by electron cryo-microscopy. |
| Authors | Carsten Sachse, Nikolaus Grigorieff, Marcus Fändrich MRC Laboratory of Molecular Biology, Cambridge, UK. |
| Keywords |  Alzheimer Disease (metabolism), Amyloid (chemistry), Cryoelectron Microscopy, Humans, Nanotechnology, Protein Folding |
| Links | DOI: 10.1002/anie.200904781, PubMed: 20069616, PMC: PMC2913414 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5132.map ( map file in CCP4 format, 322 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 = 96 A , B = 240 A , C = 48 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2.4 A , Y = 2.4 A , Z = 2.4 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Cross-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 |
 Sample | |
| Name | Human Abeta (1-40) |
|---|---|
| Number of Components | 1 |
| Oligomeric State | helical |
| Theoretical Mass | 0.004330 MDa |
| Component #1: protein - Abeta | |
| Scientific name | Abeta |
| Scientific Name of Species | Homo sapiens (NCBI Taxonomy: 9606) |
| Common Name of Species | Human |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Helical Parameters | Axial Symmetry: s2 Delta Z: 4.8 A Hand: LEFT HANDED |
|---|---|
| Staining | Blot for 7 seconds before plunging |
| Specimen Conc | 1 mg/ml |
| Specimen Support Details | Quantifoil 400 mesh 1.3 micrometer holes |
| Specimen State | filament |
| Buffer | pH: 8.7 Details: 50 mM Borate |
| Vitrification | |
| Method | Blot for 7 seconds before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: custom-built plunging apparatus. in coldroom at 277 K. |
| Instrument | HOMEMADE PLUNGER |
| Temperature | 77.2 Kelvin |
| Imaging | |
| Microscope | FEI TECNAI F30 |
| Date | 09-Nov-2005 |
| 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: 58333 X |
| Astigmatism | objective lens astigmatism was corrected at 200,000 times magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1900 nm - 3500 nm |
| Specimen Holder | |
| Holder | Side entry liquid nitrogen-cooled cryo specimen holder ( GATAN LIQUID NITROGEN ) |
| Temperature | 93 Kelvin |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 62 |
| Sampling Size | 7 microns |
 Processing | |
| Method | helical reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | iterative algebraic reconstruction |
| Euler Angles Details | one-degree sampling around helical axis, out-of-plane tilt 16 degree deviation (in 1 degree steps) |
| Software | SPIDER |
| CTF Correction | Each particle CTFTILT |
| Resolution By Author | 10.1 |
| Resolution Method | 10.1 |
| Helical | |
| Details | The 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 data | emd_5132.map.gz (285.4 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5132 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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