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Refined structure of the nicotinic acetycholine receptor at 4A resolution.

RCSB Protein Data Bank PDB ID: 2OKJ  primary research article cited below:

REFINED STRUCTURE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR AT 4A RESOLUTION.

Unwin, N.
Journal: (2005) J.Mol.Biol. 346: 967
PubMed: 15701510  
DOI: 10.1016/j.jmb.2004.12.031  
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Figure 1.  Acetylcholine Receptor (PDB ID: 2BG9) imported and annotated in Sketchfab

PubMed Abstract:

We present a refined model of the membrane-associated Torpedo acetylcholine (ACh) receptor at 4A resolution. An improvedexperimental density map was obtained from 342 electron images of helical tubes, and the refined structure was derived to an R-factor of 36.7% (R(free) 37.9%) by standard crystallographic methods, after placing the densities corresponding to a singlemolecule into an artificial unit cell. The agreement between experimental and calculated phases along the helical layer-lines wasused to monitor progress in the refinement and to give an independent measure of the accuracy. The atomic model allowed adetailed description of the whole receptor in the closed-channel form, including the ligand-binding and intracellular domains, which have not previously been interpreted at a chemical level. We confirm that the two ligand-binding alpha subunits have a differentextended conformation from the three other subunits in the closed channel, and identify several interactions on both pairs ofsubunit interfaces, and within the alpha subunits, which may be responsible for their “distorted” structures. The ACh-coordinatingamino acid side-chains of the alpha subunits are far apart in the closed channel, indicating that a localised rearrangement,involving closure of loops B and C around the bound ACh molecule, occurs upon activation. A comparison of the structure of thealpha subunit with that of AChBP having ligand present, suggests how the localised rearrangement overcomes the distortions andinitiates the rotational movements associated with opening of the channel. Both vestibules of the channel are stronglyelectronegative, providing a cation-stabilising environment at either entrance of the membrane pore. Access to the pore on theintracellular side is further influenced by narrow lateral windows, which would be expected to screen out electrostatically ions of thewrong charge and size.

Importing RCSB Protein Databank Files into  Sketchfab

RCSB Protein Data Bank file PDB ID: 2BG9 was downloaded and imported into UCSF-CHIMERA.    The models were uploaded to Sketchfab (SF) directly from Chimera, using the Chimera-SF plugin (currently in beta-testing phase).

Once the model was imported into Sketchfab, lighting and background image were adjusted.  The surface protein was made semi-transparent using the SF material editor. The  generated embed code was copied and pasted onto this page (see Fig. 1).

Once the model was imported, lighting and background image were adjusted.  The  generated embed code was copied and pasted onto this page (see Fig. 1).  Click the “Play” button to start the interactivity.

Use the arrows located on the bottom of the viewer ( arows) to navigate to the various positions.  The mouse wheel is used to zoom in or out.

AchR was also featured in Dr. David Goodsell’s Molecule of the Month:

Acetylcholine Receptor

November 2005 Molecule of the Month by David Goodsell

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Importing RCSB Protein Databank Files into  Sketchfab

RCSB Protein Data Bank file PDB ID: 8CAT was downloaded and imported into UCSF-CHIMERA.    The models were uploaded to Sketchfab (SF) directly from Chimera, using the Chimera-SF plugin (currently in beta-testing phase).

Once the model was imported into Sketchfab, lighting and background image were adjusted.  The surface protein was made semi-transparent using the SF material editor. The  generated embed code was copied and pasted onto this page (see Fig. 1).