User:Alice Harmon/Notes - Revision history

Jaime Prilusky at 18:20, 26 July 2014

2014-07-26T18:20:45Z

←Older revision		Revision as of 18:20, 26 July 2014
Line 6:		Line 6:
	===Multiple frames on a page===		===Multiple frames on a page===
	To direct a green link to a specific frame do this: <br>		To direct a green link to a specific frame do this: <br>
-	1. name the frame. instead of <applet load='3ku2' , write \|<applet name='left' load='3ku2' <br>	+	1. name the frame. instead of <applet load='3ku2' , write \|<applet name='left' load='3ku2' <br>
-	2. add the frame name to the green link. Instead of ><scene name='56/562377/Holo-ikinase/1'>, write <scene name='56/562377/Holo-ikinase/1' target='left'>	+	2. add the frame name to the green link. Instead of <scene name='56/562377/Holo-ikinase/1'>, write <scene name='56/562377/Holo-ikinase/1' target='left'>

Alice Harmon at 13:57, 26 July 2014

2014-07-26T13:57:32Z

←Older revision		Revision as of 13:57, 26 July 2014
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	<nowiki><ref name = "Fujii2007"/></nowiki>		<nowiki><ref name = "Fujii2007"/></nowiki>
	<nowiki><ref>PMID:12805596</ref></nowiki>		<nowiki><ref>PMID:12805596</ref></nowiki>
		+
		+	===Multiple frames on a page===
		+	To direct a green link to a specific frame do this: <br>
		+	1. name the frame. instead of <applet load='3ku2' , write \|<applet name='left' load='3ku2' <br>
		+	2. add the frame name to the green link. Instead of ><scene name='56/562377/Holo-ikinase/1'>, write <scene name='56/562377/Holo-ikinase/1' target='left'>

Alice Harmon at 00:54, 7 October 2013

2013-10-07T00:54:49Z

←Older revision		Revision as of 00:54, 7 October 2013
Line 45:		Line 45:
	<scene name='55/559985/Aposnrk2_6/5'>Cysteines in space fill kinase</scene><br>		<scene name='55/559985/Aposnrk2_6/5'>Cysteines in space fill kinase</scene><br>
	<scene name='55/559985/Ost1hab1/1'>Cysteines in the complex</scene>		<scene name='55/559985/Ost1hab1/1'>Cysteines in the complex</scene>
		+
		+	==PP2C==
		+	Sheen PMID:9448270
		+	Greengard PMID:16509582
		+	http://en.wikipedia.org/wiki/Phosphatase

Alice Harmon at 21:01, 6 October 2013

2013-10-06T21:01:01Z

←Older revision		Revision as of 21:01, 6 October 2013
Line 11:		Line 11:
	also http://en.wikipedia.org/wiki/Calmodulin<br>		also http://en.wikipedia.org/wiki/Calmodulin<br>
	see Proteopedia:Policy		see Proteopedia:Policy
		+
		+	ABI1 and ABI2 were discovered in genetic screens for mutants that were ABA insensitive. HAB1, HAB2, were discovered ... and PP2CA/AHG3. They are members of clade A of the plant protein phosphatase 2C family, and each has a C-terminal protein phosphatase 2C domain, and an N-terminal variable sequence<ref name = "Schweighofer2004">PMID:15130549</ref>.
		+
		+	PP2c catalytic domains have 11 conserved subdomains <ref>PMID:8819174</ref>.

	Truncations of the noncatalytic N-terminal		Truncations of the noncatalytic N-terminal

Alice Harmon at 20:53, 6 October 2013

2013-10-06T20:53:32Z

←Older revision		Revision as of 20:53, 6 October 2013
Line 12:		Line 12:
	see Proteopedia:Policy		see Proteopedia:Policy

-		+	Truncations of the noncatalytic N-terminal
		+	part of Arabidopsis PP2Cs ABI1 had only minor effects on
		+	phosphatase activity.Bertauche, N. et al. (1996) Protein phosphatase activity of abscisic acid
		+	insensitive 1 (ABI1) protein from Arabidopsis thaliana. Eur.
		+	J. Biochem. 241, 193–200

Alice Harmon at 18:13, 5 October 2013

2013-10-05T18:13:45Z

←Older revision		Revision as of 18:13, 5 October 2013
Line 1:		Line 1:
		+	===Ref tag examples===
		+	<nowiki><ref name = "Mustilli2002">PMID:12468729</ref></nowiki>
		+	<nowiki><ref name = "Fujii2007"/></nowiki>
		+	<nowiki><ref>PMID:12805596</ref></nowiki>
		+
		+
	===Pages needed===		===Pages needed===
	edit calmodulin pages<Br>		edit calmodulin pages<Br>
Line 5:		Line 11:
	also http://en.wikipedia.org/wiki/Calmodulin<br>		also http://en.wikipedia.org/wiki/Calmodulin<br>
	see Proteopedia:Policy		see Proteopedia:Policy
-	For PYR-ABI1 page:
-	===PP2C structures===

-	~~[[1a6q]] – hPP2C <br />~~	+
-	~~[[2iq1]] – hPP2C κ <br />~~	+
-	~~[[2p8e]] – hPP2C β<br />~~	+
-	~~[[2cm1]] – PP2C + Mn – Micobacterium tuberculosis<br />~~	+
-	~~[[3d8k]] – PP2C – Toxoplasma gondii<br />~~	+
-	~~[[3jrq]], [[3kdj]], [[3nmn]] – AtPP2C + Pyl1 – Arabidopsis thaliana<br />~~	+
-	~~[[3nmt]], [[3kb3]], [[3nmv]], [[3ujl]] – AtPP2C + Pyl2<br />~~	+
-	~~[[4ds8]] – AtPP2C + Pyl3 + Mn<br />~~	+
-	~~[[3rt0]] – AtPP2C (mutant) + Pyl10<br />~~	+
-	~~[[3qn1]], [[3zvu]] – AtPP2C + Pyr1<br />~~	+
-	~~[[3ujg]] – AtPP2C + SNRK2<br />~~	+
-	~~[[3ujk]] – AtPP2C <br />~~	+

Alice Harmon at 14:20, 5 October 2013

2013-10-05T14:20:26Z

←Older revision		Revision as of 14:20, 5 October 2013
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	[[3ujk]] – AtPP2C <br />		[[3ujk]] – AtPP2C <br />

-	===Pyr/PYL/RCAR structures===
-
-	'''APO structures'''<br>
-
-	[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>
-	[[3kay]], apo AtPYL1 <br>
-	[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>
-	[[3klx]], apo ATPYL3<br>
-	[[4jdl]], Apo PYL5<br>
-	[[3rt2]], [[3uqh]] apo PYL10<br>
-
-
-
-	'''Structures with (+)-ABA'''<br>
-	[[3k90]], PYR1.ABA<br>
-	[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>
-	[[3jrs]], AtPYL1.ABA<br>
-	[[3kdi]], [[3kb0]] AtPYL2.ABA<br>
-	[[4dsb]], [[4dsc]] AtPYL3 with ABA<br>
-	[[3oqu]], PYL9.ABA<br>
-	[[3r6p]], PYL10.ABA<br>
-
-
-
-	'''Structures with (-)-ABA'''<br>
-	[[4jda]], PYL3 with (-)-ABA<br>
-
-
-	'''Structures with pyrabactin'''<br>
-	[[3njo]], PYR1.Pyrabactin<br>
-	[[3nef]], [[3neg]], [[3nr4]] PYL1.pyrabactin<br>
-	[[3nj0]], [[3ns2]] PYL2.Pyrabactin<br>
-	[[3nj1]], PYL2 V114I mutant.Pyrabactin <br>
-	[[3nmh]], AtPYL2 in complex with pyrabactin<br>
-	[[3nmp]], AtPYL2 mutant A93F in complex with pyrabactin<br>
-	[[3oji]], PYL3 with pyrabactin(?)<br>
-
-
-	'''Structures with (+)-ABA or homolog and a PP2C'''<br>
-	[[3qn1]], PYR1.ABA - HAB1<br>
-	[[3zvu]], PYR1 H60P mutant .ABA - HAB1<br>
-	[[3kb3]], AtPYL1.ABA in complex with HAB1<br>
-	[[3jrq]], [[3kdj]] AtPYL1.ABA in complex with ABI1<br>
-	[[3ujl]], PYL2.ABA - ABI2<br>
-	[[4lga]], [[4lgb]] PYL2.ABA mimic- HAB1<br>
-	[[4ds8]], AtPYL3.ABA complex with HAB1
-	[[3rt0]], PYL10.ABA - HAB1<br>
-
-
-	'''Structures with pyrabactin and a PP2C'''<br>
-	[[4la7]], [[4lg5]] PYL2.Quinabactin - HAB1<br>
-	[[3nmn]], AtPYL1.pyrabactin in complex with ABI1<br>
-	[[3nmt]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase HAB1<br>
-	[[3nmv]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase ABI1<br>

Alice Harmon at 19:40, 4 October 2013

2013-10-04T19:40:22Z

←Older revision		Revision as of 19:40, 4 October 2013
Line 29:		Line 29:
	[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>		[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>
	[[3klx]], apo ATPYL3<br>		[[3klx]], apo ATPYL3<br>
-	[[~~4JDL~~]], Apo PYL5<br>	+	[[4jdl]], Apo PYL5<br>
-	[[~~3RT2~~]], [[~~3UQH~~]] apo PYL10<br>	+	[[3rt2]], [[3uqh]] apo PYL10<br>



	'''Structures with (+)-ABA'''<br>		'''Structures with (+)-ABA'''<br>
-	[[~~3K90~~]], PYR1.ABA<br>	+	[[3k90]], PYR1.ABA<br>
	[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>		[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>
	[[3jrs]], AtPYL1.ABA<br>		[[3jrs]], AtPYL1.ABA<br>
	[[3kdi]], [[3kb0]] AtPYL2.ABA<br>		[[3kdi]], [[3kb0]] AtPYL2.ABA<br>
	[[4dsb]], [[4dsc]] AtPYL3 with ABA<br>		[[4dsb]], [[4dsc]] AtPYL3 with ABA<br>
-	[[~~3OQU~~]], PYL9.ABA<br>	+	[[3oqu]], PYL9.ABA<br>
-	[[~~3R6P~~]], PYL10.ABA<br>	+	[[3r6p]], PYL10.ABA<br>



	'''Structures with (-)-ABA'''<br>		'''Structures with (-)-ABA'''<br>
-	[[~~4JDA~~]], PYL3 with (-)-ABA<br>	+	[[4jda]], PYL3 with (-)-ABA<br>


	'''Structures with pyrabactin'''<br>		'''Structures with pyrabactin'''<br>
-	[[~~3NJO~~]], PYR1.Pyrabactin<br>	+	[[3njo]], PYR1.Pyrabactin<br>
-	[[~~3NEF~~]], [[~~3NEG~~]], [[~~3NR4~~]] PYL1.pyrabactin<br>	+	[[3nef]], [[3neg]], [[3nr4]] PYL1.pyrabactin<br>
-	[[~~3NJ0~~]], [[~~3NS2~~]] PYL2.Pyrabactin<br>	+	[[3nj0]], [[3ns2]] PYL2.Pyrabactin<br>
-	[[~~3NJ1~~]], PYL2 V114I mutant.Pyrabactin <br>	+	[[3nj1]], PYL2 V114I mutant.Pyrabactin <br>
	[[3nmh]], AtPYL2 in complex with pyrabactin<br>		[[3nmh]], AtPYL2 in complex with pyrabactin<br>
	[[3nmp]], AtPYL2 mutant A93F in complex with pyrabactin<br>		[[3nmp]], AtPYL2 mutant A93F in complex with pyrabactin<br>
Line 60:		Line 60:

	'''Structures with (+)-ABA or homolog and a PP2C'''<br>		'''Structures with (+)-ABA or homolog and a PP2C'''<br>
-	[[~~3QN1~~]], PYR1.ABA - HAB1<br>	+	[[3qn1]], PYR1.ABA - HAB1<br>
-	[[~~3ZVU~~]], PYR1 H60P mutant .ABA - HAB1<br>	+	[[3zvu]], PYR1 H60P mutant .ABA - HAB1<br>
	[[3kb3]], AtPYL1.ABA in complex with HAB1<br>		[[3kb3]], AtPYL1.ABA in complex with HAB1<br>
	[[3jrq]], [[3kdj]] AtPYL1.ABA in complex with ABI1<br>		[[3jrq]], [[3kdj]] AtPYL1.ABA in complex with ABI1<br>
-	[[~~3UJL~~]], PYL2.ABA - ABI2<br>	+	[[3ujl]], PYL2.ABA - ABI2<br>
-	[[~~4LGA~~]], [[~~4LGB~~]] PYL2.ABA mimic- HAB1<br>	+	[[4lga]], [[4lgb]] PYL2.ABA mimic- HAB1<br>
	[[4ds8]], AtPYL3.ABA complex with HAB1		[[4ds8]], AtPYL3.ABA complex with HAB1
-	[[~~3RT0~~]], PYL10.ABA - HAB1<br>	+	[[3rt0]], PYL10.ABA - HAB1<br>


	'''Structures with pyrabactin and a PP2C'''<br>		'''Structures with pyrabactin and a PP2C'''<br>
-	[[~~4LA7~~]], [[~~4LG5~~]] PYL2.Quinabactin - HAB1<br>	+	[[4la7]], [[4lg5]] PYL2.Quinabactin - HAB1<br>
	[[3nmn]], AtPYL1.pyrabactin in complex with ABI1<br>		[[3nmn]], AtPYL1.pyrabactin in complex with ABI1<br>
	[[3nmt]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase HAB1<br>		[[3nmt]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase HAB1<br>

Alice Harmon at 19:31, 4 October 2013

2013-10-04T19:31:59Z

←Older revision		Revision as of 19:31, 4 October 2013
Line 23:		Line 23:
	===Pyr/PYL/RCAR structures===		===Pyr/PYL/RCAR structures===

-	[[3kay]] apo AtPYL1 <br>	+	'''APO structures'''<br>
		+
		+	[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>
		+	[[3kay]], apo AtPYL1 <br>
	[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>		[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>
-	[[3klx]] apo ATPYL3<br>	+	[[3klx]], apo ATPYL3<br>
		+	[[4JDL]], Apo PYL5<br>
		+	[[3RT2]], [[3UQH]] apo PYL10<br>

-	[[3k3k]] AtPyr1 dimer, one monomor is bound to ABA and the other unliganded

-	[[3jrs]] AtPYL1 in complex with ABA<br>
-	[[3kdi]], [[3kb0]] AtPYL2 in complex with ABA<br>
-	[[3nmh]] AtPYL2 in complex with pyrabactin<br>
-	[[3nmp]] AtPYL2 mutant A93F in complex with pyrabactin<br>
-	[[4dsb]], [[4dsb]], [[4dsc]] AtPYL3 with ABA<br>
-	[[3oji]] PYL3 with pyrabactin(?)<br>

-	[[~~3nmn~~]] AtPYL1.pyrabactin in complex with ~~ABI1~~<br>	+	'''Structures with (+)-ABA'''<br>
		+	[[3K90]], PYR1.ABA<br>
		+	[[3k3k]], AtPyr1 dimer, one monomer is bound to ABA and the other unliganded<br>
		+	[[3jrs]], AtPYL1.ABA<br>
		+	[[3kdi]], [[3kb0]] AtPYL2.ABA<br>
		+	[[4dsb]], [[4dsc]] AtPYL3 with ABA<br>
		+	[[3OQU]], PYL9.ABA<br>
		+	[[3R6P]], PYL10.ABA<br>
		+
		+
		+
		+	'''Structures with (-)-ABA'''<br>
		+	[[4JDA]], PYL3 with (-)-ABA<br>
		+
		+
		+	'''Structures with pyrabactin'''<br>
		+	[[3NJO]], PYR1.Pyrabactin<br>
		+	[[3NEF]], [[3NEG]], [[3NR4]] PYL1.pyrabactin<br>
		+	[[3NJ0]], [[3NS2]] PYL2.Pyrabactin<br>
		+	[[3NJ1]], PYL2 V114I mutant.Pyrabactin <br>
		+	[[3nmh]], AtPYL2 in complex with pyrabactin<br>
		+	[[3nmp]], AtPYL2 mutant A93F in complex with pyrabactin<br>
		+	[[3oji]], PYL3 with pyrabactin(?)<br>
		+
		+
		+	'''Structures with (+)-ABA or homolog and a PP2C'''<br>
		+	[[3QN1]], PYR1.ABA - HAB1<br>
		+	[[3ZVU]], PYR1 H60P mutant .ABA - HAB1<br>
		+	[[3kb3]], AtPYL1.ABA in complex with HAB1<br>
	[[3jrq]], [[3kdj]] AtPYL1.ABA in complex with ABI1<br>		[[3jrq]], [[3kdj]] AtPYL1.ABA in complex with ABI1<br>
-	[[~~3kb3~~]] ~~AtPYL1~~.ABA in complex with HAB1<br>	+	[[3UJL]], PYL2.ABA - ABI2<br>
-	[[3nmt]] AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase HAB1<br>	+	[[4LGA]], [[4LGB]] PYL2.ABA mimic- HAB1<br>
-	[[3nmv]] AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase ABI1	+	[[4ds8]], AtPYL3.ABA complex with HAB1
-	~~[[4ds8]] AtPYL3.ABA complex with PP2C 16~~	+	[[3RT0]], PYL10.ABA - HAB1<br>
		+
		+
		+	'''Structures with pyrabactin and a PP2C'''<br>
		+	[[4LA7]], [[4LG5]] PYL2.Quinabactin - HAB1<br>
		+	[[3nmn]], AtPYL1.pyrabactin in complex with ABI1<br>
		+	[[3nmt]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase HAB1<br>
		+	[[3nmv]], AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase ABI1<br>
		+

	==add link to kinase domain page on==		==add link to kinase domain page on==

Alice Harmon at 18:32, 4 October 2013

2013-10-04T18:32:06Z

←Older revision		Revision as of 18:32, 4 October 2013
Line 22:		Line 22:

	===Pyr/PYL/RCAR structures===		===Pyr/PYL/RCAR structures===
		+
	[[3kay]] apo AtPYL1 <br>		[[3kay]] apo AtPYL1 <br>
-	[[3kdh]], [[3kaz]] apo AtPYL2<br>	+	[[3kdh]], [[3kaz]], [[3kl1]] apo AtPYL2<br>
		+	[[3klx]] apo ATPYL3<br>

-	[[~~3K3K~~]] AtPyr1 dimer, one monomor is bound to ABA and the other unliganded	+	[[3k3k]] AtPyr1 dimer, one monomor is bound to ABA and the other unliganded

	[[3jrs]] AtPYL1 in complex with ABA<br>		[[3jrs]] AtPYL1 in complex with ABA<br>
Line 31:		Line 33:
	[[3nmh]] AtPYL2 in complex with pyrabactin<br>		[[3nmh]] AtPYL2 in complex with pyrabactin<br>
	[[3nmp]] AtPYL2 mutant A93F in complex with pyrabactin<br>		[[3nmp]] AtPYL2 mutant A93F in complex with pyrabactin<br>
		+	[[4dsb]], [[4dsb]], [[4dsc]] AtPYL3 with ABA<br>
		+	[[3oji]] PYL3 with pyrabactin(?)<br>

	[[3nmn]] AtPYL1.pyrabactin in complex with ABI1<br>		[[3nmn]] AtPYL1.pyrabactin in complex with ABI1<br>
Line 37:		Line 41:
	[[3nmt]] AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase HAB1<br>		[[3nmt]] AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase HAB1<br>
	[[3nmv]] AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase ABI1		[[3nmv]] AtPYL2 mutant A93F.pyrabactin in complex with type 2C protein phosphatase ABI1
		+	[[4ds8]] AtPYL3.ABA complex with PP2C 16

	==add link to kinase domain page on==		==add link to kinase domain page on==