1shi: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1shi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Stichodactyla_helianthus Stichodactyla helianthus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SHI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SHI FirstGlance]. <br> | <table><tr><td colspan='2'>[[1shi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Stichodactyla_helianthus Stichodactyla helianthus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SHI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SHI FirstGlance]. <br> | ||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr> | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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=1shi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1shi OCA], [https://pdbe.org/1shi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1shi RCSB], [https://www.ebi.ac.uk/pdbsum/1shi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1shi 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=1shi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1shi OCA], [https://pdbe.org/1shi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1shi RCSB], [https://www.ebi.ac.uk/pdbsum/1shi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1shi ProSAT]</span></td></tr> | ||
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<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sh/1shi_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sh/1shi_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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=1shi ConSurf]. | </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=1shi ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A high resolution structure in solution has been determined for the polypeptide neurotoxin I, from the sea anemone Stichodactyla helianthus, using NMR data, distance geometry calculations, and refinement by back-calculation of two-dimensional nuclear Overhauser enhancement (NOE) spectra. A set of 913 distance constraints derived from NOEs was used, together with a large set of lower distance bounds based on the absence of NOEs in the spectrum. Eight published structures for neurotoxin I were refined independently to give structures which agree better with the experimental data, as reflected in reduced R factors calculated over well resolved cross-peaks of the two-dimensional NOE spectra and a lower total volume of peaks in back-calculated spectra that are absent from experimental spectra. The refined structures are also more precisely defined, with mean pairwise root mean square differences over backbone heavy atoms of 0.62 A for well defined residues and 1.14 A for all residues, compared with previous values of 1.09 and 2.41 A, respectively. The consensus constraint set from the 8 refined structures was also used to generate 12 new structures, with corresponding root mean square differences of 0.76 and 1.26 A. In all 20 structures the loop linking the first and second strands of the beta-sheet is considerably better defined than before. A type I beta-turn encompassing the functionally important residues Asp6, Asp7, and Glu8 is evident in the refined structures. | |||
Refined structure in solution of the sea anemone neurotoxin ShI.,Wilcox GR, Fogh RH, Norton RS J Biol Chem. 1993 Nov 25;268(33):24707-19. PMID:7901218<ref>PMID:7901218</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1shi" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
Latest revision as of 10:26, 9 October 2024
REFINED STRUCTURE IN SOLUTION OF THE SEA ANEMONE NEUROTOXIN SHIREFINED STRUCTURE IN SOLUTION OF THE SEA ANEMONE NEUROTOXIN SHI
Structural highlights
FunctionNA21_STIHL Binds specifically to voltage-gated sodium channels (Nav), thereby delaying their inactivation during signal transduction (By similarity). Is highly toxic to crabs (by intrahemocoelic injection) (PubMed:2568126, PubMed:22015268), but without effect upon mice (by intraperitoneal injection) (PubMed:2568126).[1] [2] 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 PubMedA high resolution structure in solution has been determined for the polypeptide neurotoxin I, from the sea anemone Stichodactyla helianthus, using NMR data, distance geometry calculations, and refinement by back-calculation of two-dimensional nuclear Overhauser enhancement (NOE) spectra. A set of 913 distance constraints derived from NOEs was used, together with a large set of lower distance bounds based on the absence of NOEs in the spectrum. Eight published structures for neurotoxin I were refined independently to give structures which agree better with the experimental data, as reflected in reduced R factors calculated over well resolved cross-peaks of the two-dimensional NOE spectra and a lower total volume of peaks in back-calculated spectra that are absent from experimental spectra. The refined structures are also more precisely defined, with mean pairwise root mean square differences over backbone heavy atoms of 0.62 A for well defined residues and 1.14 A for all residues, compared with previous values of 1.09 and 2.41 A, respectively. The consensus constraint set from the 8 refined structures was also used to generate 12 new structures, with corresponding root mean square differences of 0.76 and 1.26 A. In all 20 structures the loop linking the first and second strands of the beta-sheet is considerably better defined than before. A type I beta-turn encompassing the functionally important residues Asp6, Asp7, and Glu8 is evident in the refined structures. Refined structure in solution of the sea anemone neurotoxin ShI.,Wilcox GR, Fogh RH, Norton RS J Biol Chem. 1993 Nov 25;268(33):24707-19. PMID:7901218[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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