User:Alice Harmon/Notes
From Proteopedia
| (7 intermediate revisions not shown.) | |||
| 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> | ||
| + | |||
| + | ===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'> | ||
| + | |||
| + | |||
===Pages needed=== | ===Pages needed=== | ||
edit calmodulin pages<Br> | edit calmodulin pages<Br> | ||
| Line 5: | Line 16: | ||
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=== | ||
| - | + | 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 | |
| + | 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 | ||
| - | [[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> | ||
| Line 98: | Line 50: | ||
<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 | ||
Current revision
Contents |
Ref tag examples
<ref name = "Mustilli2002">PMID:12468729</ref> <ref name = "Fujii2007"/> <ref>PMID:12805596</ref>
Multiple frames on a page
To direct a green link to a specific frame do this:
1. name the frame. instead of <applet load='3ku2' , write |<applet name='left' load='3ku2'
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'>
Pages needed
edit calmodulin pages
edit Ca2+/Calmodulin dependent protein kinase page
Create CaM-binding motifs
also http://en.wikipedia.org/wiki/Calmodulin
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[1].
PP2c catalytic domains have 11 conserved subdomains [2].
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
add link to kinase domain page on
PKA pages
Goodsells PKA article on PDB website
Editing issues
HTML tags don't work inside scene tags:
superscript works fine here: Ca2+-bound CAD
but not here:
|
In the green tag, the tag Ca<sup>2+</sup> and the text before it are not rendered.
headings that are in scrollable sections are not included in the the page index
Can load scene using a different structure into a frame, but can't change the caption of the frame.
ABA signaling
Clearest picture of Pyr1 gate - latch is in Annu Reviews article
unused:
PP2C
Sheen PMID:9448270 Greengard PMID:16509582 http://en.wikipedia.org/wiki/Phosphatase
