5o4f

From Proteopedia

(Difference between revisions)

Current revision

Structure of GluK3 ligand-binding domain (S1S2) in complex with the agonist LM-12b at 2.10 A resolution

Structural highlights

5o4f is a 2 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 2.1Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GRIK3_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. The postsynaptic actions of Glu are mediated by a variety of receptors that are named according to their selective agonists. This receptor binds domoate > kainate >> L-glutamate = quisqualate >> AMPA = NMDA.^[1]

Publication Abstract from PubMed

Ionotropic glutamate receptors (iGluRs) are involved in most of the fast excitatory synaptic transmission in the central nervous system. These receptors are important for learning and memory formation, but are also involved in the development of diseases such as Alzheimer's disease, epilepsy and depression. To understand the function of different types of iGluRs, selective agonists are invaluable as pharmacological tool compounds. Here, we report binding affinities of two bicyclic, conformationally restricted analogues of glutamate (CIP-AS and LM-12b) at AMPA (GluA2 and GluA3) and kainate receptor subunits (GluK1-3 and GluK5). Both CIP-AS and LM-12b were found to be GluK3-preferring agonists, with Ki of 6 and 22 nM, respectively, at recombinant GluK3 receptors. The detailed binding mode of CIP-AS and LM-12b in the ligand-binding domains of the AMPA receptor subunit GluA2 (GluA2-LBD) and the kainate receptor subunits GluK1 (GluK1-LBD) and GluK3 (GluK3-LBD) was investigated by X-ray crystallography. CIP-AS stabilized all three receptor constructs in conformations similar to those with kainate. Remarkably, whereas LM-12b bound in a similar manner to CIP-AS in GluA2-LBD and GluK3-LBD, it introduced full closure of the ligand-binding domain in GluK1-LBD and formation of a D1-D2 interlobe hydrogen bond between Glu441 and Ser721, as also observed with glutamate. As the binding affinity of LM-12b at GluK1 is approximately 8-fold better than that for CIP-AS (Ki of 85 and 656 nM, respectively), it shows that small changes in agonist structure can lead to prominent differences in structure and function.

Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors.,Mollerud S, Pinto A, Marconi L, Frydenvang K, Thorsen TS, Laulumaa S, Venskutonyte R, Winther S, Moral AMC, Tamborini L, Conti P, Pickering DS, Kastrup JS ACS Chem Neurosci. 2017 Sep 20;8(9):2056-2064. doi: 10.1021/acschemneuro.7b00201., Epub 2017 Jul 21. PMID:28691798^[2]

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

References

↑ Venskutonyte R, Frydenvang K, Gajhede M, Bunch L, Pickering DS, Kastrup JS. Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate. J Struct Biol. 2011 Sep 1. PMID:21907808 doi:10.1016/j.jsb.2011.08.014
↑ Mollerud S, Pinto A, Marconi L, Frydenvang K, Thorsen TS, Laulumaa S, Venskutonyte R, Winther S, Moral AMC, Tamborini L, Conti P, Pickering DS, Kastrup JS. Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors. ACS Chem Neurosci. 2017 Sep 20;8(9):2056-2064. doi: 10.1021/acschemneuro.7b00201., Epub 2017 Jul 21. PMID:28691798 doi:http://dx.doi.org/10.1021/acschemneuro.7b00201

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5o4f"

Categories: Large Structures | Rattus norvegicus | Frydenvang K | Kastrup JS | Moellerud S

@@ Line 1: / Line 1: @@
 ==Structure of GluK3 ligand-binding domain (S1S2) in complex with the agonist LM-12b at 2.10 A resolution==
-<StructureSection load='5o4f' size='340' side='right' caption='[[5o4f]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='5o4f' size='340' side='right'caption='[[5o4f]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5o4f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O4F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O4F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5o4f]] is a 2 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=5O4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O4F FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8VE:(3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic+acid'>8VE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5o4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o4f OCA], [http://pdbe.org/5o4f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o4f RCSB], [http://www.ebi.ac.uk/pdbsum/5o4f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o4f ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8VE:(3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic+acid'>8VE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5o4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o4f OCA], [https://pdbe.org/5o4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o4f RCSB], [https://www.ebi.ac.uk/pdbsum/5o4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o4f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GRIK3_RAT GRIK3_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. The postsynaptic actions of Glu are mediated by a variety of receptors that are named according to their selective agonists. This receptor binds domoate > kainate >> L-glutamate = quisqualate >> AMPA = NMDA.<ref>PMID:21907808</ref>
+[https://www.uniprot.org/uniprot/GRIK3_RAT GRIK3_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. The postsynaptic actions of Glu are mediated by a variety of receptors that are named according to their selective agonists. This receptor binds domoate > kainate >> L-glutamate = quisqualate >> AMPA = NMDA.<ref>PMID:21907808</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 5o4f" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Glutamate receptor 3D structures|Glutamate receptor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Frydenvang, K]]
+[[Category: Large Structures]]
-[[Category: Kastrup, J S]]
+[[Category: Rattus norvegicus]]
-[[Category: Moellerud, S]]
+[[Category: Frydenvang K]]
-[[Category: Agonist]]
+[[Category: Kastrup JS]]
-[[Category: Gluk3]]
+[[Category: Moellerud S]]
-[[Category: Glur7]]
-[[Category: Ionotropic glutamate receptor]]
-[[Category: Kainate receptor]]
-[[Category: Ligand-binding domain]]
-[[Category: Membrane protein]]

5o4f

From Proteopedia

Current revision

Structure of GluK3 ligand-binding domain (S1S2) in complex with the agonist LM-12b at 2.10 A resolution

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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