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2kgi
From Proteopedia
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==Solution structure of JARID1A C-terminal PHD finger in complex with H3(1-9)K4me3== | ==Solution structure of JARID1A C-terminal PHD finger in complex with H3(1-9)K4me3== | ||
| - | <StructureSection load='2kgi' size='340' side='right' caption='[[2kgi]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2kgi' size='340' side='right'caption='[[2kgi]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2kgi]] is a 2 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[2kgi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KGI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KGI FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>< | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr> | + | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">JARID1A, RBBP2, RBP2 ([ | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">JARID1A, RBBP2, RBP2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kgi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kgi OCA], [https://pdbe.org/2kgi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kgi RCSB], [https://www.ebi.ac.uk/pdbsum/2kgi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kgi ProSAT]</span></td></tr> |
| - | <table> | + | </table> |
| + | == Function == | ||
| + | [[https://www.uniprot.org/uniprot/KDM5A_HUMAN KDM5A_HUMAN]] Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May stimulate transcription mediated by nuclear receptors. May be involved in transcriptional regulation of Hox proteins during cell differentiation. May participate in transcriptional repression of cytokines such as CXCL12. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. In a histone demethylase-independent manner, acts as a coactivator of the CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER1/2 and other clock-controlled genes and increases histone acetylation at PER1/2 promoters by inhibiting the activity of HDAC1 (By similarity).[UniProtKB:Q3UXZ9]<ref>PMID:11358960</ref> <ref>PMID:15949438</ref> <ref>PMID:17320160</ref> <ref>PMID:17320161</ref> <ref>PMID:17320163</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kg/2kgi_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kg/2kgi_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/ | + | </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=2kgi ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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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 2kgi" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
| - | *[[Retinoblastoma-binding protein|Retinoblastoma-binding protein]] | + | *[[Lysine-specific histone demethylase 3D structures|Lysine-specific histone demethylase 3D structures]] |
| + | *[[Retinoblastoma-binding protein 3D structures|Retinoblastoma-binding protein 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Human]] |
| - | [[Category: Patel, D J | + | [[Category: Large Structures]] |
| - | [[Category: Song, J | + | [[Category: Patel, D J]] |
| - | [[Category: Wang, Z | + | [[Category: Song, J]] |
| + | [[Category: Wang, Z]] | ||
| + | [[Category: Alternative splicing]] | ||
[[Category: Chromatin regulator]] | [[Category: Chromatin regulator]] | ||
[[Category: Developmental protein]] | [[Category: Developmental protein]] | ||
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[[Category: Phd finger]] | [[Category: Phd finger]] | ||
[[Category: Phosphoprotein]] | [[Category: Phosphoprotein]] | ||
| + | [[Category: Polymorphism]] | ||
[[Category: Transcription]] | [[Category: Transcription]] | ||
[[Category: Transcription regulation]] | [[Category: Transcription regulation]] | ||
| + | [[Category: Zinc]] | ||
[[Category: Zinc-finger]] | [[Category: Zinc-finger]] | ||
Current revision
Solution structure of JARID1A C-terminal PHD finger in complex with H3(1-9)K4me3
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Categories: Human | Large Structures | Patel, D J | Song, J | Wang, Z | Alternative splicing | Chromatin regulator | Developmental protein | Dioxygenase | Histone modification | Iron | Jarid1a | Leukemia | Metal binding protein | Metal-binding | Nucleus | Oxidoreductase | Phd finger | Phosphoprotein | Polymorphism | Transcription | Transcription regulation | Zinc | Zinc-finger
