|Entry||Database: PDB / ID: 6bnu|
|Title||Structure of bare actin filament, backbone-averaged with sidechains truncated to alanine|
|Components||Actin, alpha skeletal muscle|
|Keywords||CONTRACTILE PROTEIN / Cytoskeleton / Filament|
|Function / homology||Actin, conserved site / Actin/actin-like conserved site / Actin family / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / Actin / positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding ...Actin, conserved site / Actin/actin-like conserved site / Actin family / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / Actin / positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / troponin I binding / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle / filamentous actin / actin monomer binding / skeletal muscle fiber development / actin filament bundle assembly / skeletal muscle myofibril / stress fiber / titin binding / actin filament polymerization / actin filament / filopodium / cell body / calcium-dependent protein binding / lamellipodium / protein domain specific binding / positive regulation of gene expression / magnesium ion binding / calcium ion binding / ATP binding / identical protein binding / cytoplasm / Actin, alpha skeletal muscle|
Function and homology information
|Specimen source||Oryctolagus cuniculus (rabbit)|
|Method||ELECTRON MICROSCOPY / helical reconstruction / cryo EM / 7.5 Å resolution|
|Authors||Gurel, P.S. / Alushin, G.A.|
|Citation||Journal: Nat Nanotechnol / Year: 2018|
Title: Controllable molecular motors engineered from myosin and RNA.
Authors: Tosan Omabegho / Pinar S Gurel / Clarence Y Cheng / Laura Y Kim / Paul V Ruijgrok / Rhiju Das / Gregory M Alushin / Zev Bryant
SummaryFull reportAbout validation report
|Date||Deposition: Nov 17, 2017 / Release: Jan 10, 2018|
|Structure viewer||Molecule: |
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 (rabbit) / References: UniProt: P68135
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: helical reconstruction|
|Component||Name: Bare actin filament / Type: COMPLEX / Entity ID: 1 / Source: NATURAL|
|Molecular weight||Value: 0.042 MDa / Experimental value: NO|
|Source (natural)||Organism: Oryctolagus cuniculus (rabbit)|
|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 FIELDBright-field microscopy / 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 / Width: 3838 / Height: 3710 / Movie frames/image: 24 / Used frames/image: 1-24|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: -166.65 deg. / Axial rise/subunit: 28.11 Å / Axial symmetry: C1|
|3D reconstruction||Resolution: 7.5 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: Atomistic model was backbone-averaged in Phenix; side chains were truncated to alanine. This treatment has resulted in the errors noted in the associated caveats.|
Overall b value: 350 / Ref protocol: FLEXIBLE FIT / Ref space: REAL
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