User:Wayne Decatur/Sandbox Glutamate receptor: Difference between revisions

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The [http://en.wikipedia.org/wiki/Glutamate_receptor glutamate receptor]is the ion channel opened by glutamate that keeps neurons in touch by mediating fast cell-to-cell information transfer in the nervous system. Several studies have revealed structures for portions of the glutamate receptor <ref name="r80">PMID: 19461580</ref><ref name="r14">PMID: 19465914</ref><ref name="r22">PMID: 19910922</ref><ref>PMID: 9804426</ref>. Groundbreaking work elucidated the structure of a complete functional, homomeric glutamate receptor<ref name="main">PMID:19946266</ref><ref>PMID: 20010675</ref> and that structure, [[3kg2]], is the subject of this page.  
The [http://en.wikipedia.org/wiki/Glutamate_receptor glutamate receptor]is the ion channel opened by glutamate that keeps neurons in touch by mediating fast cell-to-cell information transfer in the nervous system. Several studies have revealed structures for portions of the glutamate receptor <ref name="r80">PMID: 19461580</ref><ref name="r14">PMID: 19465914</ref><ref name="r22">PMID: 19910922</ref><ref>PMID: 9804426</ref>. Groundbreaking work elucidated the structure of a complete functional, homomeric glutamate receptor<ref name="main">PMID:19946266</ref><ref>PMID: 20010675</ref> and that structure, [[3kg2]], is the subject of this page.  
==Structure of the Glutamate Receptor (GluA2)==
==Structure of the Glutamate Receptor (GluA2)==
The homomeric rat GluA2 receptor <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1'>has four subunits</scene> arranged in a 'Y'-shape with the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Meas3kg2/1'>'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.&nbsp;{{Link Toggle FancyCartoonHighQualityView}}.
{{Structure
{{Structure
|PDB= 3kg2 |SIZE=400|SCENE=User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1|CAPTION= glutamate receptor ([[3kg2]]), resolution 3.6&Aring; (<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1'>initial scene</scene>)
|PDB= 3kg2 |SIZE=400|SCENE=User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1|CAPTION= glutamate receptor ([[3kg2]]), resolution 3.6&Aring; (<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1'>initial scene</scene>)
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|RELATEDENTRY=
|RELATEDENTRY=
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kg2 OCA], [http://www.ebi.ac.uk/pdbsum/3kg2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3kg2 RCSB]</span>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kg2 OCA], [http://www.ebi.ac.uk/pdbsum/3kg2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3kg2 RCSB]</span>
}}
}}The homomeric rat GluA2 receptor <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Default3kg2/1'>has four subunits</scene> arranged in a 'Y'-shape with the <scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Meas3kg2/1'>'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.&nbsp;{{Link Toggle FancyCartoonHighQualityView}}.
 
===Domains===
===Domains===
The subunits themselves are modular <ref>PMID: 7539962</ref>and the major domains are found in layers in the tetrameric structure.
The subunits themselves are modular <ref>PMID: 7539962</ref>and the major domains are found in layers in the tetrameric structure.
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*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmdatobsuper/1'>Superposition of the TMD</scene>.
*<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Tmdatobsuper/1'>Superposition of the TMD</scene>.


<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atobmorph/2'>Subunit A morphing into Subunit B best illustrates how portions of the protein change</scene> between the two conformational forms.<br>
<scene name='User:Wayne_Decatur/Sandbox_Glutamate_receptor/Atobmorph/2'>Subunit A morphing into Subunit B best illustrates how portions, especially the linkers, of the protein change</scene> between the two conformational forms.<br>
{{Button Toggle AnimationOnPause}}
{{Button Toggle AnimationOnPause}}
: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.
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::Note that the M4 segment associates with the ion-channel core of an adjacent subunit.
::Note that the M4 segment associates with the ion-channel core of an adjacent subunit.
:{{Link Toggle FancyCartoonHighQualityView}}.
:{{Link Toggle FancyCartoonHighQualityView}}.
*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==
==Details of Structure Featured==
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* [[2a5t]] – GluN1-GluN2A ligand-binding domain heterodimer
* [[2a5t]] – GluN1-GluN2A ligand-binding domain heterodimer
* [[2a5s]] – GluN2A ligand-binding domain bound with glutamate
* [[2a5s]] – GluN2A ligand-binding domain bound with glutamate
* [[3h5w]] – and [[3h5v]] Crystal structure of the GluR2 amino-terminal domain<ref name="r80" />
* [[3h5w]] and [[3h5v]] – Crystal structure of the GluR2 amino-terminal domain<ref name="r80" />
* [[1gr2]] – Structure of a glutamate-receptor ligand-binding core in complex with kainate<ref>PMID: 9804426</ref>
* [[1gr2]] – Structure of a glutamate-receptor ligand-binding core in complex with kainate<ref>PMID: 9804426</ref>
* [[3jpy]] – and [[3jpw]] Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit<ref name="r22" />
* [[3jpy]] and [[3jpw]] – Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit<ref name="r22" />
* [[1iiw]] and [[1iit]] and [[1ii5]]  – Prokaryotic glutamte receptor (Glur0) Apo structure and with various ligands bound, including glutmate <ref>PMID: 10617203</ref>. This helped cement the notion the glutamate and potassium receptors share structural similarity and possibly evolutionary ancestry <ref name="pot1" /><ref name="pot2" />.
* [[3hgh]] and [[3hgh]] – The N-terminal domain of a GluR6-subtype glutamate receptor<ref name="r14" />
* [[3hgh]] and [[3hgh]] – The N-terminal domain of a GluR6-subtype glutamate receptor<ref name="r14" />
* [[1jq2]] – ''Streptomyces lividans'' KcsA potassium channel<ref>PMID: 9525859</ref>: The M1, M2 and M3 segments of GluA2's ion channel overlap remarkably well with the structurally equivalent portions KcsA.  
* [[1bl8]] and [[1jq1]] and [[1jq2]] – ''Streptomyces lividans'' KcsA potassium channel<ref name="pot3" /><ref>PMID:11573095</ref>: The M1, M2 and M3 segments of GluA2's ion channel overlap remarkably well with the structurally equivalent portions KcsA.  
* [[Molecular Playground/Glutamate Receptor]]
* [[Molecular Playground/Glutamate Receptor]]


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* [http://www.nature.com/nature/journal/v462/n7274/covers/ Glutamate Receptor on the cover] of [http://www.nature.com/ Nature]
* [http://www.nature.com/nature/journal/v462/n7274/covers/ Glutamate Receptor on the cover] of [http://www.nature.com/ Nature]
* [http://en.wikipedia.org/wiki/Glutamate_receptor Glutamate receptor Wikipedia entry]
* [http://en.wikipedia.org/wiki/Glutamate_receptor Glutamate receptor Wikipedia entry]
* [http://www.bristol.ac.uk/synaptic/receptors/#ionotropic Glutamate Receptors page] at the [http://www.bristol.ac.uk/synaptic/ MRC Centre for Synaptic Plasticity at the University of Bristol]


''Page started with original page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 16 11:24:54 2009 for [[3kg2]].''
''Page started with original page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 16 11:24:54 2009 for [[3kg2]].''
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[[Category: Neuron]]
[[Category: Neuron]]
[[Category: Neurotransmitter]]
[[Category: Neurotransmitter]]
[[Category: Potassium Channels]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Streptomyces lividans]]
[[Category: Cabral, J M.]]
[[Category: Chait, B T.]]
[[Category: Cohen, S L.]]
[[Category: Doyle, D A.]]
[[Category: Gulbis, J M.]]
[[Category: Kuo, A.]]
[[Category: Mackinnon, R.]]
[[Category: Pfuetzner, R A.]]
[[Category: Integral membrane protein]]
[[Category: Potassium channel]]
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