1shi: Difference between revisions

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{{Seed}}
[[Image:1shi.png|left|200px]]


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==REFINED STRUCTURE IN SOLUTION OF THE SEA ANEMONE NEUROTOXIN SHI==
The line below this paragraph, containing "STRUCTURE_1shi", creates the "Structure Box" on the page.
<StructureSection load='1shi' size='340' side='right'caption='[[1shi]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
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<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>
{{STRUCTURE_1shi|  PDB=1shi  |  SCENE=  }}
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NA21_STIHL NA21_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).<ref>PMID:22015268</ref> <ref>PMID:2568126</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <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/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </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].
<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===
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_7901218}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1shi" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 7901218 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_7901218}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1SHI is a [[Single protein]] structure of sequence from [http://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].
 
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/7901218 7901218]
[[Category: Single protein]]
[[Category: Stichodactyla helianthus]]
[[Category: Stichodactyla helianthus]]
[[Category: Dyke, T R.]]
[[Category: Dyke TR]]
[[Category: Norton, R S.]]
[[Category: Norton RS]]
[[Category: Pallaghy, P K.]]
[[Category: Pallaghy PK]]
[[Category: Neurotoxin]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 02:23:36 2008''

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

1shi is a 1 chain structure with sequence from Stichodactyla helianthus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR, 20 models
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NA21_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 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[3]

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

References

  1. ↑ Rodríguez AA, Cassoli JS, Sa F, Dong ZQ, de Freitas JC, Pimenta AM, de Lima ME, Konno K, Lee SM, Garateix A, Zaharenko AJ. Peptide fingerprinting of the neurotoxic fractions isolated from the secretions of sea anemones Stichodactyla helianthus and Bunodosoma granulifera. New members of the APETx-like family identified by a 454 pyrosequencing approach. Peptides. 2012 Mar;34(1):26-38. PMID:22015268 doi:10.1016/j.peptides.2011.10.011
  2. ↑ Kem WR, Parten B, Pennington MW, Price DA, Dunn BM. Isolation, characterization, and amino acid sequence of a polypeptide neurotoxin occurring in the sea anemone Stichodactyla helianthus. Biochemistry. 1989 Apr 18;28(8):3483-9. PMID:2568126 doi:10.1021/bi00434a050
  3. ↑ Wilcox GR, Fogh RH, Norton RS. Refined structure in solution of the sea anemone neurotoxin ShI. J Biol Chem. 1993 Nov 25;268(33):24707-19. PMID:7901218
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