2g2m - Revision history

OCA at 14:39, 29 December 2021

OCA — Wed, 29 Dec 2021 14:39:16 GMT

←Older revision		Revision as of 14:39, 29 December 2021
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	<StructureSection load='2g2m' size='340' side='right'caption='[[2g2m]]' scene=''>		<StructureSection load='2g2m' size='340' side='right'caption='[[2g2m]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2G2M FirstGlance]. <br>	+	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G2M FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2g2m FirstGlance], [~~http~~://www.ebi.ac.uk/pdbsum/2g2m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2g2m ProSAT]</span></td></tr>	+	</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=2g2m FirstGlance], [https://www.ebi.ac.uk/pdbsum/2g2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g2m ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:08, 27 March 2020

OCA — Fri, 27 Mar 2020 11:08:01 GMT

←Older revision		Revision as of 11:08, 27 March 2020
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	==MODEL OF NUCLEOTIDE BINDING PROTEIN FROM CAENORHABDITIS ELEGANS ALSO CALLED CED4==		==MODEL OF NUCLEOTIDE BINDING PROTEIN FROM CAENORHABDITIS ELEGANS ALSO CALLED CED4==
-	<StructureSection load='2g2m' size='340' side='right' caption='[[2g2m]]' scene=''>	+	<StructureSection load='2g2m' size='340' side='right'caption='[[2g2m]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G2M FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G2M FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Theoretical Model]]		[[Category: Theoretical Model]]
		+	[[Category: Large Structures]]
	[[Category: Chattopadhyaya, R]]		[[Category: Chattopadhyaya, R]]
	[[Category: Pal, A]]		[[Category: Pal, A]]

OCA at 06:45, 20 June 2018

OCA — Wed, 20 Jun 2018 06:45:34 GMT

←Older revision		Revision as of 06:45, 20 June 2018
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G2M FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G2M FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g2m FirstGlance], [http://www.ebi.ac.uk/pdbsum/2g2m PDBsum]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g2m FirstGlance], [http://www.ebi.ac.uk/pdbsum/2g2m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2g2m ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:38, 11 February 2016

OCA — Thu, 11 Feb 2016 10:38:17 GMT

←Older revision		Revision as of 10:38, 11 February 2016
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		+	{{Theoretical_model}}
		+
	==MODEL OF NUCLEOTIDE BINDING PROTEIN FROM CAENORHABDITIS ELEGANS ALSO CALLED CED4==		==MODEL OF NUCLEOTIDE BINDING PROTEIN FROM CAENORHABDITIS ELEGANS ALSO CALLED CED4==
	<StructureSection load='2g2m' size='340' side='right' caption='[[2g2m]]' scene=''>		<StructureSection load='2g2m' size='340' side='right' caption='[[2g2m]]' scene=''>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Theoretical Model]]
	[[Category: Chattopadhyaya, R]]		[[Category: Chattopadhyaya, R]]
	[[Category: Pal, A]]		[[Category: Pal, A]]

OCA at 14:42, 10 September 2015

OCA — Thu, 10 Sep 2015 14:42:23 GMT

←Older revision		Revision as of 14:42, 10 September 2015
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2g2m" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:59, 16 January 2015

OCA — Fri, 16 Jan 2015 07:59:35 GMT

←Older revision		Revision as of 07:59, 16 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G2M FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G2M FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g2m FirstGlance], [http://www.ebi.ac.uk/pdbsum/2g2m PDBsum]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g2m FirstGlance], [http://www.ebi.ac.uk/pdbsum/2g2m PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 05:30, 29 September 2014

OCA — Mon, 29 Sep 2014 05:30:32 GMT

←Older revision		Revision as of 05:30, 29 September 2014
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-	~~{{Theoretical_model}}~~	+	==MODEL OF NUCLEOTIDE BINDING PROTEIN FROM CAENORHABDITIS ELEGANS ALSO CALLED CED4==
		+	<StructureSection load='2g2m' size='340' side='right' caption='[[2g2m]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2G2M FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2g2m FirstGlance], [http://www.ebi.ac.uk/pdbsum/2g2m PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Three dimensional models of NB-ARC domains in five different proteins were constructed based on the recently published crystal structure of the apoptotic protease activating factor 1, of which two are for tomato species, one each for flax, Arabidopsis, and nematode. Standard multiple sequence alignment was performed for chosen members of the NB-ARC domains, very divergent from each other in protein sequence, followed by homology model building and structure refinement. In this alignment, amino acid insertions and deletions between members generally fall in loop regions or at ends of alpha helices. Despite the presence of sequence divergence between the species, it is argued that the NB-ARC domains carry out the similar biological functions in the various species, highlighting the ATP binding and ATPase activity. By our comparative study of these models, it is predicted that NB-ARC domains should bind ADP/ATP rather than GDP/GTP. Both natural and induced mutants of Arabidopsis within the RPS2 locus and their phenotypes for disease reaction against Pseudomonas syringae are rationalized from the protein model. Apaf-1 Thr263 and Arg265 positions conserved totally within the NB-ARC domains are predicted to take active part in the catalytic activity of kinase-3 motif, the arginine known as the sensor I motif in AAA+ proteins. This was later verified for the Ced-4 crystal structure in complex with Ced-9. Our model of Ced-4 based on Apaf-1 was also compared with its crystal structure in the Ced-4-Ced-9 complex; the 3 layered alpha/beta domain superposes quite well, helical domain I is shifted by about 5 A but the winged helix domain is rotated away to a new position. Since Apaf-1 was crystallized with ADP and Ced-4-Ced9 with magnesium-ATP, this rotation signifies a change in structure of these NB-ARC domains between the two forms. Further, we hypothesize that certain mutants in the plant R proteins called 'constitutive gain-of-function' or 'autocatalytic' dispose their winged helix domains permanently like the magnesium-ATP form as observed for Ced-4, avoiding the closed ADP conformation. The models are also validated with mutagenesis data for a related tomato protein I-2, tomato prf and flax, including loss of function, wild type and autocatalytic phenotypes, and compared with similar data for potato and tobacco proteins, for which models were not built. These three dimensional models would help us to understand the spatial arrangement, function of R proteins and their conserved motifs.

-	~~[[Image~~:~~2g2m~~.~~png\|left\|200px]]~~	+	Three-dimensional Models of NB-ARC Domains of Disease Resistance Proteins in Tomato, Arabidopsis, and Flax (p. 357-372).,Chattopadhyaya R, Pal A J Biomol Struct Dyn. 2008 Feb;25(4):357-72. PMID:18092830<ref>PMID:18092830</ref>

-	~~{{STRUCTURE_2g2m\| PDB=2g2m \| SCENE= }}~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	==~~=MODEL OF NUCLEOTIDE BINDING PROTEIN FROM CAENORHABDITIS ELEGANS ALSO CALLED CED4===~~	+	== References ==
-		+	<references/>
-	~~{{ABSTRACT_PUBMED_18092830}}~~	+	__TOC__
-		+	</StructureSection>
-	~~==Reference~~==	+
-	<~~ref group="xtra">PMID:018092830<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Chattopadhyaya, R]]		[[Category: Chattopadhyaya, R]]
	[[Category: Pal, A]]		[[Category: Pal, A]]

OCA: Protected "2g2m" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 08:44:59 GMT

Protected "2g2m" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:44, 21 October 2012

OCA at 08:44, 21 October 2012

OCA — Sun, 21 Oct 2012 08:44:56 GMT

←Older revision		Revision as of 08:44, 21 October 2012
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	{{Theoretical_model}}		{{Theoretical_model}}
-	~~{{Seed}}~~	+
	[[Image:2g2m.png\|left\|200px]]		[[Image:2g2m.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2g2m", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2g2m\| PDB=2g2m \| SCENE= }}		{{STRUCTURE_2g2m\| PDB=2g2m \| SCENE= }}

	===MODEL OF NUCLEOTIDE BINDING PROTEIN FROM CAENORHABDITIS ELEGANS ALSO CALLED CED4===		===MODEL OF NUCLEOTIDE BINDING PROTEIN FROM CAENORHABDITIS ELEGANS ALSO CALLED CED4===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18092830}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18092830 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18092830}}		{{ABSTRACT_PUBMED_18092830}}
-
-	==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G2M OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18092830~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018092830</ref><references group="xtra"/>
	[[Category: Chattopadhyaya, R]]		[[Category: Chattopadhyaya, R]]
	[[Category: Pal, A]]		[[Category: Pal, A]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 8 06:48:26 2010''

OCA at 03:48, 8 April 2010

OCA — Thu, 08 Apr 2010 03:48:27 GMT

←Older revision		Revision as of 03:48, 8 April 2010
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-	~~'''Theoretical Model'''~~	+	{{Theoretical_model}}
		+	{{Seed}}
		+	[[Image:2g2m.png\|left\|200px]]

-	The ~~entry 2G2M~~ is ~~a Theoretical Model titled 'Model of nucleotide binding protein from Caenorhabditis elegans also called ced4'~~.	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2g2m", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_2g2m\| PDB=2g2m \| SCENE= }}

-	~~[[Category:Theoretical Model]]~~	+	===MODEL OF NUCLEOTIDE BINDING PROTEIN FROM CAENORHABDITIS ELEGANS ALSO CALLED CED4===


-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 30 09~~:56:~~45 2008~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18092830}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18092830 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18092830}}
		+
		+	==About this Structure==
		+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2G2M OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:18092830</ref><references group="xtra"/>
		+	[[Category: Chattopadhyaya, R]]
		+	[[Category: Pal, A]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 8 06:48:26 2010''