6mmp: Difference between revisions

Latest revision as of 11:08, 17 October 2024

Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 0.1 millimolar EDTA, and at pH 8.0Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 0.1 millimolar EDTA, and at pH 8.0

6mmp, resolution 6.88Å

Structural highlights

6mmp is a 4 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:	Electron Microscopy, Resolution 6.88Å
Ligands:
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

N-methyl-D-aspartate receptors (NMDARs) play essential roles in memory formation, neuronal plasticity, and brain development, with their dysfunction linked to a range of disorders from ischemia to schizophrenia. Zinc and pH are physiological allosteric modulators of NMDARs, with GluN2A-containing receptors inhibited by nanomolar concentrations of divalent zinc and by excursions to low pH. Despite the widespread importance of zinc and proton modulation of NMDARs, the molecular mechanism by which these ions modulate receptor activity has proven elusive. Here, we use cryoelectron microscopy to elucidate the structure of the GluN1/GluN2A NMDAR in a large ensemble of conformations under a range of physiologically relevant zinc and proton concentrations. We show how zinc binding to the amino terminal domain elicits structural changes that are transduced though the ligand-binding domain and result in constriction of the ion channel gate.

Mechanisms for Zinc and Proton Inhibition of the GluN1/GluN2A NMDA Receptor.,Jalali-Yazdi F, Chowdhury S, Yoshioka C, Gouaux E Cell. 2018 Nov 29;175(6):1520-1532.e15. doi: 10.1016/j.cell.2018.10.043. PMID:30500536^[1]

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

References

↑ Jalali-Yazdi F, Chowdhury S, Yoshioka C, Gouaux E. Mechanisms for Zinc and Proton Inhibition of the GluN1/GluN2A NMDA Receptor. Cell. 2018 Nov 29;175(6):1520-1532.e15. doi: 10.1016/j.cell.2018.10.043. PMID:30500536 doi:http://dx.doi.org/10.1016/j.cell.2018.10.043

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OCA

[1] Jalali-Yazdi F, Chowdhury S, Yoshioka C, Gouaux E. Mechanisms for Zinc and Proton Inhibition of the GluN1/GluN2A NMDA Receptor. Cell. 2018 Nov 29;175(6):1520-1532.e15. doi: 10.1016/j.cell.2018.10.043. PMID:30500536 doi:http://dx.doi.org/10.1016/j.cell.2018.10.043

[1]

@@ Line 3: / Line 3: @@
 <SX load='6mmp' size='340' side='right' viewer='molstar' caption='[[6mmp]], [[Resolution|resolution]] 6.88&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6mmp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MMP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6mmp]] is a 4 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=6MMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MMP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 6.88&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Grin1, Nmdar1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat]), Grin2a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=6mmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mmp OCA], [http://pdbe.org/6mmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mmp RCSB], [http://www.ebi.ac.uk/pdbsum/6mmp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mmp ProSAT]</span></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=6mmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mmp OCA], [https://pdbe.org/6mmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mmp RCSB], [https://www.ebi.ac.uk/pdbsum/6mmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mmp ProSAT]</span></td></tr>
 </table>
-== Function ==
-[[http://www.uniprot.org/uniprot/NMDZ1_RAT NMDZ1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Mediated by glycine. Plays a key role in synaptic plasticity, synaptogenesis, excitotoxicity, memory acquisition and learning. It mediates neuronal functions in glutamate neurotransmission. Is involved in the cell surface targeting of NMDA receptors.<ref>PMID:15996549</ref>  [[http://www.uniprot.org/uniprot/NMDE1_RAT NMDE1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Activation requires binding of agonist to both types of subunits.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 24: @@
 __TOC__
 </SX>
-[[Category: Buffalo rat]]
 [[Category: Large Structures]]
-[[Category: Chowdhury, S]]
+[[Category: Rattus norvegicus]]
-[[Category: Gouaux, E]]
+[[Category: Chowdhury S]]
-[[Category: Jalali-Yazdi, F]]
+[[Category: Gouaux E]]
-[[Category: Yoshioka, C]]
+[[Category: Jalali-Yazdi F]]
-[[Category: Ionotropic glutamate receptor]]
+[[Category: Yoshioka C]]
-[[Category: Ligand-gated ion channel]]
-[[Category: Membrane protein]]
-[[Category: Nmda receptor]]
-[[Category: Transport protein]]

6mmp: Difference between revisions

Latest revision as of 11:08, 17 October 2024

Structural highlights

Publication Abstract from PubMed

See Also

References

Contents

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6mmp: Difference between revisions

Latest revision as of 11:08, 17 October 2024

Structural highlights

Publication Abstract from PubMed

See Also

References

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