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6dk0

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Human sigma-1 receptor bound to NE-100

Structural highlights

6dk0 is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

SGMR1_HUMAN Juvenile amyotrophic lateral sclerosis. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.

Function

SGMR1_HUMAN Functions in lipid transport from the endoplasmic reticulum and is involved in a wide array of cellular functions probably through regulation of the biogenesis of lipid microdomains at the plasma membrane. Involved in the regulation of different receptors it plays a role in BDNF signaling and EGF signaling. Also regulates ion channels like the potassium channel and could modulate neurotransmitter release. Plays a role in calcium signaling through modulation together with ANK2 of the ITP3R-dependent calcium efflux at the endoplasmic reticulum. Plays a role in several other cell functions including proliferation, survival and death. Originally identified for its ability to bind various psychoactive drugs it is involved in learning processes, memory and mood alteration (PubMed:16472803, PubMed:9341151). Necessary for proper mitochondrial axonal transport in motor neurons, in particular the retrograde movement of mitochondria (By similarity).[UniProtKB:O55242]^[1] ^[2]

Publication Abstract from PubMed

The sigma1 receptor is a poorly understood membrane protein expressed throughout the human body. Ligands targeting the sigma1 receptor are in clinical trials for treatment of Alzheimer's disease, ischemic stroke, and neuropathic pain. However, relatively little is known regarding the sigma1 receptor's molecular function. Here, we present crystal structures of human sigma1 receptor bound to the antagonists haloperidol and NE-100, and the agonist (+)-pentazocine, at crystallographic resolutions of 3.1 A, 2.9 A, and 3.1 A, respectively. These structures reveal a unique binding pose for the agonist. The structures and accompanying molecular dynamics (MD) simulations identify agonist-induced structural rearrangements in the receptor. Additionally, we show that ligand binding to sigma1 is a multistep process that is rate limited by receptor conformational change. We used MD simulations to reconstruct a ligand binding pathway involving two major conformational changes. These data provide a framework for understanding the molecular basis for sigma1 agonism.

Structural basis for sigma1 receptor ligand recognition.,Schmidt HR, Betz RM, Dror RO, Kruse AC Nat Struct Mol Biol. 2018 Oct;25(10):981-987. doi: 10.1038/s41594-018-0137-2., Epub 2018 Oct 5. PMID:30291362^[3]

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

References

↑ Wang L, Duncan G. Silencing of sigma-1 receptor induces cell death in human lens cells. Exp Cell Res. 2006 May 1;312(8):1439-46. Epub 2006 Feb 9. PMID:16472803 doi:http://dx.doi.org/S0014-4827(06)00008-5
↑ Jbilo O, Vidal H, Paul R, De Nys N, Bensaid M, Silve S, Carayon P, Davi D, Galiegue S, Bourrie B, Guillemot JC, Ferrara P, Loison G, Maffrand JP, Le Fur G, Casellas P. Purification and characterization of the human SR 31747A-binding protein. A nuclear membrane protein related to yeast sterol isomerase. J Biol Chem. 1997 Oct 24;272(43):27107-15. PMID:9341151
↑ Schmidt HR, Betz RM, Dror RO, Kruse AC. Structural basis for sigma1 receptor ligand recognition. Nat Struct Mol Biol. 2018 Oct;25(10):981-987. doi: 10.1038/s41594-018-0137-2., Epub 2018 Oct 5. PMID:30291362 doi:http://dx.doi.org/10.1038/s41594-018-0137-2

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6dk0"

Categories: Homo sapiens | Large Structures | Kruse AC | Schmidt HR

@@ Line 1: / Line 1: @@
 ==Human sigma-1 receptor bound to NE-100==
-<StructureSection load='6dk0' size='340' side='right' caption='[[6dk0]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='6dk0' size='340' side='right'caption='[[6dk0]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6dk0]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DK0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DK0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6dk0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DK0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GKY:N-{2-[4-methoxy-3-(2-phenylethoxy)phenyl]ethyl}-N-propylpropan-1-amine'>GKY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.9&#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=6dk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dk0 OCA], [http://pdbe.org/6dk0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dk0 RCSB], [http://www.ebi.ac.uk/pdbsum/6dk0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dk0 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GKY:N-{2-[4-methoxy-3-(2-phenylethoxy)phenyl]ethyl}-N-propylpropan-1-amine'>GKY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6dk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dk0 OCA], [https://pdbe.org/6dk0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dk0 RCSB], [https://www.ebi.ac.uk/pdbsum/6dk0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dk0 ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/SGMR1_HUMAN SGMR1_HUMAN]] Juvenile amyotrophic lateral sclerosis. The disease is caused by mutations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.
+[https://www.uniprot.org/uniprot/SGMR1_HUMAN SGMR1_HUMAN] Juvenile amyotrophic lateral sclerosis. The disease is caused by mutations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.
 == Function ==
-[[http://www.uniprot.org/uniprot/SGMR1_HUMAN SGMR1_HUMAN]] Functions in lipid transport from the endoplasmic reticulum and is involved in a wide array of cellular functions probably through regulation of the biogenesis of lipid microdomains at the plasma membrane. Involved in the regulation of different receptors it plays a role in BDNF signaling and EGF signaling. Also regulates ion channels like the potassium channel and could modulate neurotransmitter release. Plays a role in calcium signaling through modulation together with ANK2 of the ITP3R-dependent calcium efflux at the endoplasmic reticulum. Plays a role in several other cell functions including proliferation, survival and death. Originally identified for its ability to bind various psychoactive drugs it is involved in learning processes, memory and mood alteration (PubMed:16472803, PubMed:9341151). Necessary for proper mitochondrial axonal transport in motor neurons, in particular the retrograde movement of mitochondria (By similarity).[UniProtKB:O55242]<ref>PMID:16472803</ref> <ref>PMID:9341151</ref>
+[https://www.uniprot.org/uniprot/SGMR1_HUMAN SGMR1_HUMAN] Functions in lipid transport from the endoplasmic reticulum and is involved in a wide array of cellular functions probably through regulation of the biogenesis of lipid microdomains at the plasma membrane. Involved in the regulation of different receptors it plays a role in BDNF signaling and EGF signaling. Also regulates ion channels like the potassium channel and could modulate neurotransmitter release. Plays a role in calcium signaling through modulation together with ANK2 of the ITP3R-dependent calcium efflux at the endoplasmic reticulum. Plays a role in several other cell functions including proliferation, survival and death. Originally identified for its ability to bind various psychoactive drugs it is involved in learning processes, memory and mood alteration (PubMed:16472803, PubMed:9341151). Necessary for proper mitochondrial axonal transport in motor neurons, in particular the retrograde movement of mitochondria (By similarity).[UniProtKB:O55242]<ref>PMID:16472803</ref> <ref>PMID:9341151</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Kruse, A C]]
+[[Category: Homo sapiens]]
-[[Category: Schmidt, H R]]
+[[Category: Large Structures]]
-[[Category: Antagonist bound]]
+[[Category: Kruse AC]]
-[[Category: Membrane protein]]
+[[Category: Schmidt HR]]
-[[Category: Receptor]]
-[[Category: Sigma-1 receptor]]

6dk0

From Proteopedia

Current revision

Human sigma-1 receptor bound to NE-100

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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