3kfm

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with kainate

Structural highlights

3kfm is a 1 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GRIA4_RAT Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L-glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. In the presence of CACNG4 or CACNG7 or CACNG8, shows resensitization which is characterized by a delayed accumulation of current flux upon continued application of glutamate (By similarity).^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

AMPA receptors (AMPARs) are tetrameric ligand-gated ion channels that couple the energy of glutamate binding to the opening of a transmembrane channel. Crystallographic and electrophysiological analysis of AMPARs has suggested a coupling between (1) cleft closure in the bilobate ligand-binding domain (LBD), (2) the resulting separation of transmembrane helix attachment points across subunit dimers, and (3) agonist efficacy. In general, more efficacious agonists induce greater degrees of cleft closure and transmembrane separation than partial agonists. Several apparent violations of the cleft-closure/efficacy paradigm have emerged, although in all cases, intradimer separation remains as the driving force for channel opening. Here, we examine the structural basis of partial agonism in GluA4 AMPARs. We find that the L651V substitution enhances the relative efficacy of kainate without increasing either LBD cleft closure or transmembrane separation. Instead, the conformational change relative to the wild-type:kainate complex involves a twisting motion with the efficacy contribution opposite from that expected based on previous analyses. As a result, channel opening may involve transmembrane rearrangements with a significant rotational component. Furthermore, a two-dimensional analysis of agonist-induced GluA2 LBD motions suggests that efficacy is not a linearly varying function of lobe 2 displacement vectors, but is rather determined by specific conformational requirements of the transmembrane domains.

Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors.,Birdsey-Benson A, Gill A, Henderson LP, Madden DR J Neurosci. 2010 Jan 27;30(4):1463-70. PMID:20107073^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Pasternack A, Coleman SK, Fethiere J, Madden DR, LeCaer JP, Rossier J, Pasternack M, Keinanen K. Characterization of the functional role of the N-glycans in the AMPA receptor ligand-binding domain. J Neurochem. 2003 Mar;84(5):1184-92. PMID:12603841
↑ Gill A, Birdsey-Benson A, Jones BL, Henderson LP, Madden DR. Correlating AMPA receptor activation and cleft closure across subunits: crystal structures of the GluR4 ligand-binding domain in complex with full and partial agonists. Biochemistry. 2008 Dec 30;47(52):13831-41. PMID:19102704 doi:10.1021/bi8013196
↑ Birdsey-Benson A, Gill A, Henderson LP, Madden DR. Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors. J Neurosci. 2010 Jan 27;30(4):1463-70. PMID:20107073 doi:30/4/1463
↑ Birdsey-Benson A, Gill A, Henderson LP, Madden DR. Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors. J Neurosci. 2010 Jan 27;30(4):1463-70. PMID:20107073 doi:30/4/1463

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3kfm"

Categories: Large Structures | Rattus norvegicus | Gill A | Madden DR

@@ Line 1: / Line 1: @@
-[[Image:3kfm.png|left|200px]]
-{{STRUCTURE_3kfm|  PDB=3kfm  |  SCENE=  }}
+==Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with kainate==
+<StructureSection load='3kfm' size='340' side='right'caption='[[3kfm]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3kfm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KFM FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KAI:3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE'>KAI</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kfm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kfm OCA], [https://pdbe.org/3kfm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kfm RCSB], [https://www.ebi.ac.uk/pdbsum/3kfm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kfm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GRIA4_RAT GRIA4_RAT] Receptor for glutamate that functions as ligand-gated ion channel in the central nervous system and plays an important role in excitatory synaptic transmission. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L-glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. In the presence of CACNG4 or CACNG7 or CACNG8, shows resensitization which is characterized by a delayed accumulation of current flux upon continued application of glutamate (By similarity).<ref>PMID:12603841</ref> <ref>PMID:19102704</ref> <ref>PMID:20107073</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kf/3kfm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kfm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+AMPA receptors (AMPARs) are tetrameric ligand-gated ion channels that couple the energy of glutamate binding to the opening of a transmembrane channel. Crystallographic and electrophysiological analysis of AMPARs has suggested a coupling between (1) cleft closure in the bilobate ligand-binding domain (LBD), (2) the resulting separation of transmembrane helix attachment points across subunit dimers, and (3) agonist efficacy. In general, more efficacious agonists induce greater degrees of cleft closure and transmembrane separation than partial agonists. Several apparent violations of the cleft-closure/efficacy paradigm have emerged, although in all cases, intradimer separation remains as the driving force for channel opening. Here, we examine the structural basis of partial agonism in GluA4 AMPARs. We find that the L651V substitution enhances the relative efficacy of kainate without increasing either LBD cleft closure or transmembrane separation. Instead, the conformational change relative to the wild-type:kainate complex involves a twisting motion with the efficacy contribution opposite from that expected based on previous analyses. As a result, channel opening may involve transmembrane rearrangements with a significant rotational component. Furthermore, a two-dimensional analysis of agonist-induced GluA2 LBD motions suggests that efficacy is not a linearly varying function of lobe 2 displacement vectors, but is rather determined by specific conformational requirements of the transmembrane domains.
-===Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with kainate===
+Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors.,Birdsey-Benson A, Gill A, Henderson LP, Madden DR J Neurosci. 2010 Jan 27;30(4):1463-70. PMID:20107073<ref>PMID:20107073</ref>
-{{ABSTRACT_PUBMED_20107073}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3kfm" style="background-color:#fffaf0;"></div>
-[[3kfm]] is a 1 chain structure with sequence 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=3KFM OCA].
 ==See Also==
-*[[Ionotropic Glutamate Receptors|Ionotropic Glutamate Receptors]]
+*[[Glutamate receptor 3D structures|Glutamate receptor 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020107073</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Rattus norvegicus]]
-[[Category: Gill, A.]]
+[[Category: Gill A]]
-[[Category: Madden, D R.]]
+[[Category: Madden DR]]
-[[Category: Ampa receptor]]
-[[Category: Cell junction]]
-[[Category: Cell membrane]]
-[[Category: Glua4]]
-[[Category: Glycoprotein]]
-[[Category: Ion transport]]
-[[Category: Ionic channel]]
-[[Category: Kainate]]
-[[Category: L651v]]
-[[Category: Ligand-binding domain]]
-[[Category: Ligand-gated ion channel]]
-[[Category: Lipoprotein]]
-[[Category: Membrane]]
-[[Category: Palmitate]]
-[[Category: Postsynaptic cell membrane]]
-[[Category: Receptor]]
-[[Category: Synapse]]
-[[Category: Transmembrane]]
-[[Category: Transport]]
-[[Category: Transport protein]]

3kfm

From Proteopedia

Current revision

Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with kainate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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