|Entry||Database: PDB / ID: 6bno|
|Title||Structure of bare actin filament|
|Components||Actin, alpha skeletal muscle|
|Keywords||CONTRACTILE PROTEIN / Cytoskeleton / Filament|
|Specimen source||Oryctolagus cuniculus / mammal / Rabbit /|
|Method||Electron microscopy (5.5 Å resolution / Filament / Helical) / Transmission electron microscopy|
|Authors||Gurel, P.S. / Alushin, G.A.|
|Citation||Elife, 2017, 6|
primary. Elife, 2017, 6 Yorodumi Papers
#1. Nat Nanotechnol, 2017 Yorodumi Papers
SummaryFull reportAbout validation report
|Date||Deposition: Nov 17, 2017 / Release: Jan 10, 2018|
Downloads & links
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
Mass: 41560.266 Da / Num. of mol.: 8
Source: (natural) Oryctolagus cuniculus / mammal / Rabbit /
Tissue: Skeletal Muscle / References: UniProt: P68135
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: HELICAL|
|Component||Name: bare actin filament / Type: COMPLEX / Details: Actin filament in the ADP state / Entity ID: 1 / Source: NATURAL|
|Molecular weight||Value: 0.042 deg. / Units: MEGADALTONS / Experimental value: YES|
|Source (natural)||Organism: Oryctolagus cuniculus|
|Buffer solution||Details: Buffer was filtered through 0.44 um filter and degassed.|
|Specimen||Conc.: 0.025 mg/ml / Details: Filamentous bare actin / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: COPPER / Grid mesh size: 200 / Grid type: C-flat-1.2/1.3|
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 kelvins|
Details: Sample was applied to a glow-discharged holey carbon grid, incubated for 60 seconds and blotted for 3 seconds from the backside with filter paper.
-Electron microscopy imaging
|Microscopy||Microscope model: FEI TECNAI 20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 29000 / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm / C2 aperture diameter: 100 mm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN|
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
|Image recording||Average exposure time: 0.25 sec. / Electron dose: 1.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 442|
|Image scans||Sampling size: 5 microns / Dimension width: 3838 / Dimension height: 3710 / Movie frames/image: 24 / Used frames/image: 1-24|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: -166.6 deg. / Axial rise/subunit: 28.11 Å / Axial symmetry: C1|
|3D reconstruction||Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 63139 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: HELICAL|
|Atomic model building||Details: Initial models were assembled from 8 actins (3J8A) through rigid body docking in Chimera, followed by flexible fitting with DireX. Resulting models were subjected to MDFF.|
Overall b value: 350 / Ref protocol: FLEXIBLE FIT / Ref space: REAL
-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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