User:Angel Herraez/Sandbox 14: Difference between revisions
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==Structure of the Glutamate Receptor (GluA2)== | ==Structure of the Glutamate Receptor (GluA2)== | ||
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===Overview=== | ===Overview=== | ||
The homomeric rat GluA2 receptor <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1' target='main1STwindow'> has four subunits</scene> arranged in a 'Y'-shape with the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Meas3kg2/1' target='main1STwindow'>'top' being about three times the width of the 'bottom'</scene><ref name="main" />. This structure is a functional homotetramer of the AMPA-subtype; native ionotropic glutamate receptors are almost exclusively heterotetramers. {{Link Toggle FancyCartoonHighQualityView}}. | The homomeric rat GluA2 receptor <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1' target='main1STwindow'> has four subunits</scene> arranged in a 'Y'-shape with the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Meas3kg2/1' target='main1STwindow'>'top' being about three times the width of the 'bottom'</scene><ref name="main" />. This structure is a functional homotetramer of the AMPA-subtype; native ionotropic glutamate receptors are almost exclusively heterotetramers. {{Link Toggle FancyCartoonHighQualityView}}. | ||
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===Subunit Non-Equivalence, Transmembrane Domain Architecture and the Occluded Pore=== | ===Subunit Non-Equivalence, Transmembrane Domain Architecture and the Occluded Pore=== | ||
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The new scene 40/408027/Default3kg2a/1 is a duplicate of User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1 | The new scene 40/408027/Default3kg2a/1 is a duplicate of User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1 | ||
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===Subunit non-equivalence=== | <td> | ||
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====Subunit non-equivalence==== | |||
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 below and the morphs referred to below will show in the main window on the left: | 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 below and the morphs referred to below will show in the main window on the left: | ||
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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. | :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=== | ====Transmembrane domain architecture and the occluded pore==== | ||
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Transmemlabeled/1' target='main2NDwindow'>Transmembrane segments M1 to M4 depicted in different colors to show the approximate 4-fold rotational symmetry of the entire ion channel domain.</scene> | *<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Transmemlabeled/1' target='main2NDwindow'>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>''' | ::* '''<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' target='main2NDwindow'> superposed with the TMD domain of GluA2</scene>, specifically the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm3/1' target='main2NDwindow'>inner helix of the K+ channel aligned with the M3 segment</scene>. The <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm1/2' target='main2NDwindow'>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. | *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' target='main2NDwindow'> superposed with the TMD domain of GluA2</scene>, specifically the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm3/1' target='main2NDwindow'>inner helix of the K+ channel aligned with the M3 segment</scene>. The <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Gluvspottmdm1/2' target='main2NDwindow'>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. | ||
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==Details of Structure Featured== | ==Details of Structure Featured== | ||
