1v6p

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1v6p" size="450" color="white" frame="true" align="right" spinBox="true" caption="1v6p, resolution 0.87&Aring;" /> '''Crystal structure of...)
Current revision (00:35, 21 November 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1v6p.jpg|left|200px]]<br /><applet load="1v6p" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1v6p, resolution 0.87&Aring;" />
 
-
'''Crystal structure of Cobrotoxin'''<br />
 
-
==Overview==
+
==Crystal structure of Cobrotoxin==
-
By using single wavelength anomalous diffraction phasing based on the, anomalous signal from copper atoms, the crystal structure of atratoxin was, determined at the resolution of 1.5 A and was refined to an ultrahigh, resolution of 0.87 A. The ultrahigh resolution electron density maps, allowed the modeling of 38 amino acid residues in alternate conformations, and the location of 322 of 870 possible hydrogen atoms. To get accurate, information at the atomic level, atratoxin-b (an analog of atratoxin with, reduced toxicity) was also refined to an atomic resolution of 0.92 A. By, the sequence and structural comparison of these two atratoxins, Arg(33), and Arg(36) were identified to be critical to their varied toxicity. The, effect of copper ions on the distribution of hydrogen atoms in atratoxin, was discussed, and the interactions between copper ions and protein, residues were analyzed based on a statistical method, revealing a novel, pentahedral copper-binding motif.
+
<StructureSection load='1v6p' size='340' side='right'caption='[[1v6p]], [[Resolution|resolution]] 0.87&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1v6p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_atra Naja atra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V6P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V6P FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.87&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1v6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v6p OCA], [https://pdbe.org/1v6p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v6p RCSB], [https://www.ebi.ac.uk/pdbsum/1v6p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v6p ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/3S1CB_NAJAT 3S1CB_NAJAT] Binds to muscle nicotinic acetylcholine receptor (nAChR) and inhibit acetylcholine from binding to the receptor, thereby impairing neuromuscular transmission. Has a higher toxicity than cobrotoxin-b.
 +
== 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/v6/1v6p_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=1v6p ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
By using single wavelength anomalous diffraction phasing based on the anomalous signal from copper atoms, the crystal structure of atratoxin was determined at the resolution of 1.5 A and was refined to an ultrahigh resolution of 0.87 A. The ultrahigh resolution electron density maps allowed the modeling of 38 amino acid residues in alternate conformations and the location of 322 of 870 possible hydrogen atoms. To get accurate information at the atomic level, atratoxin-b (an analog of atratoxin with reduced toxicity) was also refined to an atomic resolution of 0.92 A. By the sequence and structural comparison of these two atratoxins, Arg(33) and Arg(36) were identified to be critical to their varied toxicity. The effect of copper ions on the distribution of hydrogen atoms in atratoxin was discussed, and the interactions between copper ions and protein residues were analyzed based on a statistical method, revealing a novel pentahedral copper-binding motif.
-
==About this Structure==
+
The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing.,Lou X, Liu Q, Tu X, Wang J, Teng M, Niu L, Schuller DJ, Huang Q, Hao Q J Biol Chem. 2004 Sep 10;279(37):39094-104. Epub 2004 Jul 12. PMID:15252034<ref>PMID:15252034</ref>
-
1V6P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Naja_atra Naja atra] with CU, CL, NA and EOH as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V6P OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
The atomic resolution crystal structure of atratoxin determined by single wavelength anomalous diffraction phasing., Lou X, Liu Q, Tu X, Wang J, Teng M, Niu L, Schuller DJ, Huang Q, Hao Q, J Biol Chem. 2004 Sep 10;279(37):39094-104. Epub 2004 Jul 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15252034 15252034]
+
</div>
 +
<div class="pdbe-citations 1v6p" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Naja atra]]
[[Category: Naja atra]]
-
[[Category: Single protein]]
+
[[Category: Hao Q]]
-
[[Category: Hao, Q.]]
+
[[Category: Huang Q]]
-
[[Category: Huang, Q.]]
+
[[Category: Liu Q]]
-
[[Category: Liu, Q.]]
+
[[Category: Lou X]]
-
[[Category: Lou, X.]]
+
[[Category: Niu L]]
-
[[Category: Niu, L.]]
+
[[Category: Teng M]]
-
[[Category: Teng, M.]]
+
[[Category: Tu X]]
-
[[Category: Tu, X.]]
+
[[Category: Wang J]]
-
[[Category: Wang, J.]]
+
-
[[Category: CL]]
+
-
[[Category: CU]]
+
-
[[Category: EOH]]
+
-
[[Category: NA]]
+
-
[[Category: atomic resolution]]
+
-
[[Category: copper ion]]
+
-
[[Category: naja atra]]
+
-
[[Category: short-chain neurotoxin]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:29:00 2007''
+

Current revision

Crystal structure of Cobrotoxin

PDB ID 1v6p

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1v6p"
Personal tools