|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||positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / skeletal muscle thin filament assembly / troponin I binding / striated muscle thin filament / actin filament bundle / Actins signature 1. / Actins signature 2. ...positive regulation of actin-dependent ATPase activity / mesenchyme migration / tropomyosin binding / myosin heavy chain binding / skeletal muscle thin filament assembly / troponin I binding / striated muscle thin filament / actin filament bundle / Actins signature 1. / Actins signature 2. / Actin, conserved site / filamentous actin / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin family / actin monomer binding / skeletal muscle fiber development / actin filament bundle assembly / skeletal muscle myofibril / stress fiber / titin binding / actin filament polymerization / actin filament / Actin / filopodium / calcium-dependent protein binding / cell body / 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 / mammal / European rabbit /|
|Method||Electron microscopy (7.5 Å resolution / Filament / Helical) / Transmission electron microscopy|
|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
Abstract: Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems or in living cells . ...Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems or in living cells . Previously, synthetic nucleic acid motors and modified natural protein motors have been developed in separate complementary strategies to achieve tunable and controllable motor function. Integrating protein and nucleic-acid components to form engineered nucleoprotein motors may enable additional sophisticated functionalities. However, this potential has only begun to be explored in pioneering work harnessing DNA scaffolds to dictate the spacing, number and composition of tethered protein motors . Here, we describe myosin motors that incorporate RNA lever arms, forming hybrid assemblies in which conformational changes in the protein motor domain are amplified and redirected by nucleic acid structures. The RNA lever arm geometry determines the speed and direction of motor transport and can be dynamically controlled using programmed transitions in the lever arm structure . We have characterized the hybrid motors using in vitro motility assays, single-molecule tracking, cryo-electron microscopy and structural probing . Our designs include nucleoprotein motors that reversibly change direction in response to oligonucleotides that drive strand-displacement reactions. In multimeric assemblies, the controllable motors walk processively along actin filaments at speeds of 10-20 nm s. Finally, to illustrate the potential for multiplexed addressable control, we demonstrate sequence-specific responses of RNA variants to oligonucleotide signals.
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 / European rabbit /
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: FILAMENT / Reconstruction method: HELICAL|
|Component||Name: Bare actin filament / Type: COMPLEX / Entity ID: 1 / Source: NATURAL|
|Molecular weight||Value: 0.042 deg. / Units: MEGADALTONS / Experimental value: NO|
|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: -166.65 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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