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6v4b

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Current revision (14:35, 6 March 2024) (edit) (undo)
 
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<StructureSection load='6v4b' size='340' side='right'caption='[[6v4b]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='6v4b' size='340' side='right'caption='[[6v4b]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6v4b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_desulfofustis_sp._pb-srb1 Uncultured desulfofustis sp. pb-srb1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V4B FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6v4b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfofustis_sp._PB-SRB1 Desulfofustis sp. PB-SRB1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V4B FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6v4a|6v4a]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">N839_03575 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1385624 uncultured Desulfofustis sp. PB-SRB1])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6v4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v4b OCA], [https://pdbe.org/6v4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v4b RCSB], [https://www.ebi.ac.uk/pdbsum/6v4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v4b 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=6v4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v4b OCA], [https://pdbe.org/6v4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v4b RCSB], [https://www.ebi.ac.uk/pdbsum/6v4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v4b ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/V4JF97_9DELT V4JF97_9DELT]
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Pentameric ligand-gated ion channels (pLGICs) are allosteric receptors that mediate rapid electrochemical signal transduction in the animal nervous system through the opening of an ion pore upon binding of neurotransmitters. Orthologs have been found and characterized in prokaryotes and they display highly similar structure-function relationships to eukaryotic pLGICs; however, they often encode greater architectural diversity involving additional amino-terminal domains (NTDs). Here we report structural, functional, and normal-mode analysis of two conformational states of a multidomain pLGIC, called DeCLIC, from a Desulfofustis deltaproteobacterium, including a periplasmic NTD fused to the conventional ligand-binding domain (LBD). X-ray structure determination revealed an NTD consisting of two jelly-roll domains interacting across each subunit interface. Binding of Ca(2+) at the LBD subunit interface was associated with a closed transmembrane pore, with resolved monovalent cations intracellular to the hydrophobic gate. Accordingly, DeCLIC-injected oocytes conducted currents only upon depletion of extracellular Ca(2+); these were insensitive to quaternary ammonium block. Furthermore, DeCLIC crystallized in the absence of Ca(2+) with a wide-open pore and remodeled periplasmic domains, including increased contacts between the NTD and classic LBD agonist-binding sites. Functional, structural, and dynamical properties of DeCLIC paralleled those of sTeLIC, a pLGIC from another symbiotic prokaryote. Based on these DeCLIC structures, we would reclassify the previous structure of bacterial ELIC (the first high-resolution structure of a pLGIC) as a "locally closed" conformation. Taken together, structures of DeCLIC in multiple conformations illustrate dramatic conformational state transitions and diverse regulatory mechanisms available to ion channels in pLGICs, particularly involving Ca(2+) modulation and periplasmic NTDs.
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Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel.,Hu H, Howard RJ, Bastolla U, Lindahl E, Delarue M Proc Natl Acad Sci U S A. 2020 Jun 1. pii: 1922701117. doi:, 10.1073/pnas.1922701117. PMID:32482881<ref>PMID:32482881</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6v4b" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Desulfofustis sp. PB-SRB1]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Uncultured desulfofustis sp. pb-srb1]]
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[[Category: Delarue M]]
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[[Category: Delarue, M]]
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[[Category: Hu HD]]
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[[Category: Hu, H D]]
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[[Category: Ion channel]]
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[[Category: N-terminal extension domain]]
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[[Category: Transport protein]]
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Current revision

DeCLIC N-terminal Domain 34-202

PDB ID 6v4b

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