User:David Canner/Sandbox glu: Difference between revisions

===Subunit non-equivalence===

<table width='240' align='left' cellpadding='2'><tr><td bgcolor='#eeeeee'><applet load='3kg2' size='240' frame='true' align='left' scene='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Ac3kg2letter/1' caption='A is equivalent to C'/></td><td bgcolor='#eeeeee'><applet load='3kg2' size='240' frame='true' align='left' scene='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Bd3kg2letter/2' caption='B is equivalent to D'/></td></tr></table>

As a result of the swapping and symmetry mismatch, there is subunit non-equivalence; even though all the chains are the same chemically, there are two distinct conformations of the subunits. This means there are two matching pairs of subunits. The pairs are illustrated on the left and the morphs referred to below will show on the right:

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:The linkers are key; besides playing roles in domain swapping and resolving the symmetry mismatch, they are also responsible for relaying the modulation signals from the ATD to the other domains and signaling the conformational change of the LBD to control the opening and closing of the pore. Beyond the two conformations seen here though this particular structure ([[3kg2]]) of the receptor does not shed light on the transduction process.

===Transmembrane domain architecture and the occluded pore===

*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Transmemlabeled/1'>Transmembrane segments M1 to M4 depicted in different colors to show the approximate 4-fold rotational symmetry of the entire ion channel domain.</scene>

::* '''<span style="color:coral">M1</span>'''

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*The TMD domain of the GluA2 receptor shares structural and sequence similarity with the pore region of the potassium (K+), as hinted at by earlier work<ref name ="pot1">PMID: 7539962</ref><ref name ="pot2">PMID: 7761417</ref><ref name ="pot3">PMID: 9525859</ref>. Here the pore region of ''Streptomyces lividans'' potassium channel ([[1bl8]])<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmd/4'> superposed with the TMD domain of GluA2</scene>, specifically the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm3/1'>inner helix of the K+ channel aligned with the M3 segment</scene>. The <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm1/2'>M1 segment of GluA2 also overlays well with the outer helix</scene> of the K+ channel even though these portions weren't even included in the calculation of the alignment seen here.

==Details of Structure Featured==

[[3kg2]] is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KG2 OCA]. Although it is billed as the first structure of a full-length glutamate receptor, the carboxy-terminal domain is not present in the structure.