|Entry||Database: PDB / ID: 6anu|
|Title||Cryo-EM structure of F-actin complexed with the beta-III-spectrin actin-binding domain|
|Keywords||STRUCTURAL PROTEIN / actin binding protein / filament|
|Specimen source||Homo sapiens / human / Wikipedia|
|Method||Electron microscopy (7 Å resolution / Filament / Helical)|
|Authors||Wang, F. / Orlova, A. / Avery, A.W. / Hays, T.S. / Egelman, E.H.|
|Citation||Nat Commun, 2017, 8, 1350-1350|
SummaryFull reportAbout validation report
|Date||Deposition: Aug 14, 2017 / Release: Nov 22, 2017|
Downloads & links
F: Actin, cytoplasmic 1
A: Actin, cytoplasmic 1
B: Actin, cytoplasmic 1
C: Actin, cytoplasmic 1
D: Actin, cytoplasmic 1
E: Actin, cytoplasmic 1
f: Spectrin beta chain, non-erythrocytic 2
a: Spectrin beta chain, non-erythrocytic 2
b: Spectrin beta chain, non-erythrocytic 2
c: Spectrin beta chain, non-erythrocytic 2
d: Spectrin beta chain, non-erythrocytic 2
e: Spectrin beta chain, non-erythrocytic 2
|Helical symmetry||Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 20 / Rise per n subunits: 27.25 Å / Rotation per n subunits: -166.87 deg.|
|Details||THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = -166.87 DEGREES RISE PER SUBUNIT (HEIGHT) = 27.25 ANGSTROMS|
Mass: 41782.660 Da / Num. of mol.: 6 / Source: (gene. exp.) Homo sapiens / human / Wikipedia / Gene: ACTB / Production host: Escherichia coli / References: UniProt: P60709
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: HELICAL|
|Component||Name: F-actin complexed with the spectrin actin-binding domain|
Type: COMPLEX / Entity ID: 1,
|Source (natural)||Organism: Homo sapiens||Source (recombinant)||Organism: Escherichia coli||Buffer solution||pH: 7.4||Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES||EM staining||Type: NEGATIVE / Material: negative stain||Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD|
|Image recording||Average exposure time: 3 sec. / Electron dose: 20 e/Å2|
Details: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the estimation of the CTF as well as for boxing filaments. Only the first two parts were used for the reconstruction (~5 electrons per Angstrom^2).
Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
|Image scans||Movie frames/image: 7|
|Software||Name: PHENIX / Version: dev_2471: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: -166.87 deg. / Axial rise/subunit: 27.25 Å / Axial symmetry: C1|
|3D reconstruction||Resolution: 7 Å / Resolution method: OTHER / Number of particles: 12443 / Algorithm: BACK PROJECTION / Details: model-map FSC 0.38 cut-off / Symmetry type: HELICAL|
|Atomic model building||Ref space: REAL|
|Refine LS restraints|
-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
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