1crf: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1crf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_atra Naja atra]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CRF FirstGlance]. <br> | <table><tr><td colspan='2'>[[1crf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Naja_atra Naja atra]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CRF 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, 12 models</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=1crf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1crf OCA], [https://pdbe.org/1crf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1crf RCSB], [https://www.ebi.ac.uk/pdbsum/1crf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1crf 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=1crf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1crf OCA], [https://pdbe.org/1crf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1crf RCSB], [https://www.ebi.ac.uk/pdbsum/1crf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1crf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cr/1crf_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cr/1crf_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=1crf 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=1crf ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The three-dimensional structure in solution of cardiotoxin II, a membrane toxin from the venom of Taiwan cobra, Naja naja atra, was determined using 1H nuclear magnetic resonance spectroscopy and molecular modeling based on the hybrid distance geometry/dynamic simulated annealing technique. A complete sequence-specific proton assignment was obtained, and the secondary structures of the protein were determined from information on nuclear Overhauser effect connectivities, coupling constants, and hydrogen exchange were confirmed using the main-chain-directed strategy. Twelve simulated annealing structures found to be within a single family were selected based on the condition of distance constraint violation less than 0.02 nm and the dihedral angle violation less than 4 degrees. The average atomic root mean square deviation between the selected structures and their geometric average are 0.079 nm for the backbone atoms and 0.137 nm for all heavy atoms; they are 0.044 nm and 0.117 nm, respectively, when considering the secondary structural residues only. The molecule adopts a compact structure consisting of three major loops emerging from a globular head. These loops contain five strands to form double- and a triple-stranded antiparallel beta sheets. Comparisons are made between this structure and those of its homologous cardiotoxins in order to derive further information on their structural variations. | |||
Cardiotoxin II from Taiwan cobra venom, Naja naja atra. Structure in solution and comparison among homologous cardiotoxins.,Bhaskaran R, Huang CC, Tsai YC, Jayaraman G, Chang DK, Yu C J Biol Chem. 1994 Sep 23;269(38):23500-8. PMID:8089116<ref>PMID:8089116</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1crf" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
Latest revision as of 09:30, 30 October 2024
CARDIOTOXIN II FROM TAIWAN COBRA VENOM, NAJA NAJA ATRA: STRUCTURE IN SOLUTION AND COMPARISION AMONG HOMOLOGOUS CARDIOTOXINSCARDIOTOXIN II FROM TAIWAN COBRA VENOM, NAJA NAJA ATRA: STRUCTURE IN SOLUTION AND COMPARISION AMONG HOMOLOGOUS CARDIOTOXINS
Structural highlights
Function3SA2_NAJAT Basic protein that binds to cell membrane and depolarizes cardiomyocytes. It also shows lytic activities, but 2-fold less important than that of CTX-A4. It binds to the integrin alpha-V/beta-3 (ITGAV/ITGB3) with a moderate affinity. It may interact with sulfatides in the cell membrane which induces pore formation and cell internalization and is responsible for cytotoxicity in cardiomyocytes. It also may target the mitochondrial membrane and induce mitochondrial swelling and fragmentation.[1] 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 PubMedThe three-dimensional structure in solution of cardiotoxin II, a membrane toxin from the venom of Taiwan cobra, Naja naja atra, was determined using 1H nuclear magnetic resonance spectroscopy and molecular modeling based on the hybrid distance geometry/dynamic simulated annealing technique. A complete sequence-specific proton assignment was obtained, and the secondary structures of the protein were determined from information on nuclear Overhauser effect connectivities, coupling constants, and hydrogen exchange were confirmed using the main-chain-directed strategy. Twelve simulated annealing structures found to be within a single family were selected based on the condition of distance constraint violation less than 0.02 nm and the dihedral angle violation less than 4 degrees. The average atomic root mean square deviation between the selected structures and their geometric average are 0.079 nm for the backbone atoms and 0.137 nm for all heavy atoms; they are 0.044 nm and 0.117 nm, respectively, when considering the secondary structural residues only. The molecule adopts a compact structure consisting of three major loops emerging from a globular head. These loops contain five strands to form double- and a triple-stranded antiparallel beta sheets. Comparisons are made between this structure and those of its homologous cardiotoxins in order to derive further information on their structural variations. Cardiotoxin II from Taiwan cobra venom, Naja naja atra. Structure in solution and comparison among homologous cardiotoxins.,Bhaskaran R, Huang CC, Tsai YC, Jayaraman G, Chang DK, Yu C J Biol Chem. 1994 Sep 23;269(38):23500-8. PMID:8089116[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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