|Entry||Database: PDB / ID: 5oqv|
|Title||Near-atomic resolution fibril structure of complete amyloid-beta(1-42) by cryo-EM|
|Descriptor||Amyloid beta A4 protein|
|Keywords||PROTEIN FIBRIL / amyloid / fibril / aggregation / Alzheimer's disease / Protein fibril|
|Specimen source||Homo sapiens / human|
|Method||Electron microscopy (4 Å resolution / Filament / Helical)|
|Authors||Gremer, L. / Schoelzel, D. / Schenk, C. / Reinartz, E. / Labahn, J. / Ravelli, R. / Tusche, M. / Lopez-Iglesias, C. / Hoyer, W. / Heise, H. / Willbold, D. / Schroeder, G.F.|
|Citation||Science, 2017, 358, 116-119|
Science, 2017, 358, 116-119 Yorodumi Papers
SummaryFull reportAbout validation report
|Date||Deposition: Aug 14, 2017 / Release: Sep 13, 2017|
Downloads & links
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein
G: Amyloid beta A4 protein
H: Amyloid beta A4 protein
I: Amyloid beta A4 protein
Mass: 4520.087 Da / Num. of mol.: 9 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P05067
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: HELICAL|
|Component||Name: Beta-amyloid protein 42 fibrils / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Homo sapiens|
|Source (recombinant)||Organism: Escherichia coli|
|Buffer solution||Details: in water / pH: 2|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: GOLD / Grid mesh size: 300 / Grid type: UltrAuFoil R 1.2/1.3 Quantifoil|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE|
Details: 2.5 microL sample was applied to the grid, blotted for 2.5 s before plunging.
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TECNAI ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 110000 / Cs: 2.7 mm|
|Image recording||Average exposure time: 2 sec. / Electron dose: 24 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2026|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: -179.275 deg. / Axial rise/subunit: 2.335 Å / Axial symmetry: C1|
|3D reconstruction||Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 127765|
Details: For the even/odd test, the fibrils were split after the final reconstruction (no gold-standard). These two half sets were then refined further independently for another 12 iterations.
Number of class averages: 1 / Symmetry type: HELICAL
|Atomic model building||Ref protocol: AB INITIO MODEL / Ref space: REAL / Target criteria: Cross-correlation coefficient|
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-Jul 12, 2017. Major update of PDB
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