6f4t

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Current revision (09:54, 23 October 2024) (edit) (undo)
 
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==Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)==
==Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)==
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<StructureSection load='6f4t' size='340' side='right' caption='[[6f4t]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
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<StructureSection load='6f4t' size='340' side='right'caption='[[6f4t]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6f4t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F4T FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6f4t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F4T FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.22&#8491;</td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6f4m|6f4m]], [[6f4n|6f4n]], [[6f4o|6f4o]], [[6f4p|6f4p]], [[6f4q|6f4q]], [[6f4r|6f4r]], [[6f4s|6f4s]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4t OCA], [https://pdbe.org/6f4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f4t RCSB], [https://www.ebi.ac.uk/pdbsum/6f4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4t ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/50S_ribosomal_protein_L16_3-hydroxylase 50S ribosomal protein L16 3-hydroxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.47 1.14.11.47] </span></td></tr>
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<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=6f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f4t OCA], [http://pdbe.org/6f4t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f4t RCSB], [http://www.ebi.ac.uk/pdbsum/6f4t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f4t ProSAT]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/KDM8_HUMAN KDM8_HUMAN]] Histone demethylase required for G2/M phase cell cycle progression. Specifically demethylates dimethylated 'Lys-36' (H3K36me2) of histone H3, an epigenetic repressive mark, thereby acting as a transcription activator. Regulates expression of CCNA1 (cyclin-A1), leading to regulate cancer cell proliferation. [[http://www.uniprot.org/uniprot/RCCD1_HUMAN RCCD1_HUMAN]] Acts as a coregulator of KDM8 to promote histone demethylase activity on di- and trimethylated 'Lys-36' (H3K36me2/me3) of histone H3 (PubMed:24981860). Plays a role in transcriptional repression of satellite repeats, possibly by regulating H3K36 methylation levels in centromeric regions together with KDM8 (PubMed:24981860). Possibly together with KDM8, involved in proper mitotic spindle organization and chromosome segregation (PubMed:24981860). Plays a role in regulating alpha-tubulin deacetylation and cytoskeletal microtubule stability and thereby promoting cell migration and TGF-beta-induced epithelial to mesenchymal transition (EMT), potentially through the inhibition of KDM8 (PubMed:28455245).<ref>PMID:24981860</ref> <ref>PMID:28455245</ref>
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[https://www.uniprot.org/uniprot/KDM8_HUMAN KDM8_HUMAN] Histone demethylase required for G2/M phase cell cycle progression. Specifically demethylates dimethylated 'Lys-36' (H3K36me2) of histone H3, an epigenetic repressive mark, thereby acting as a transcription activator. Regulates expression of CCNA1 (cyclin-A1), leading to regulate cancer cell proliferation.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
</div>
<div class="pdbe-citations 6f4t" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 6f4t" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: 50S ribosomal protein L16 3-hydroxylase]]
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[[Category: Homo sapiens]]
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[[Category: Chowdhury, R]]
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[[Category: Large Structures]]
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[[Category: Islam, M S]]
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[[Category: Chowdhury R]]
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[[Category: Schofield, C J]]
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[[Category: Islam MS]]
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[[Category: 2-oxoglutarate]]
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[[Category: Schofield CJ]]
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[[Category: 40s ribosomal protein s6]]
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[[Category: Arginine hydroxylation]]
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[[Category: Arginyl c-3 hydroxylase]]
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[[Category: Beta-hydroxylation]]
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[[Category: Cancer]]
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[[Category: Cell structure]]
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[[Category: Cytoplasm]]
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[[Category: Development]]
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[[Category: Dioxygenase]]
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[[Category: Dna-binding]]
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[[Category: Dsbh]]
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[[Category: Epigenetic regulation]]
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[[Category: Facial triad]]
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[[Category: Hydroxylation]]
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[[Category: Hypoxia]]
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[[Category: Iron]]
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[[Category: Jmjc]]
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[[Category: Jmjc demethylase]]
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[[Category: Jmjc domain]]
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[[Category: Jmjc domain-containing protein 5]]
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[[Category: Jmjc hydroxylase]]
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[[Category: Jmjd5]]
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[[Category: Kdm]]
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[[Category: Kdm8]]
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[[Category: Lysine-specific demethylase 8]]
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[[Category: Metal-binding]]
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[[Category: Non-heme]]
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[[Category: Oxidoreductase]]
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[[Category: Oxygenase]]
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[[Category: Phosphorylation]]
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[[Category: Polymorphism]]
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[[Category: Post-translational modification]]
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[[Category: Ptm]]
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[[Category: Rcc1 domain-containing protein 1]]
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[[Category: Rccd1]]
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[[Category: Regulator of chromosome condensation]]
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[[Category: Ribosome biogenesis]]
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[[Category: Rps6]]
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[[Category: Signaling]]
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[[Category: Transcription]]
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[[Category: Transcription activator/inhibitor]]
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[[Category: Translation]]
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Current revision

Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)

PDB ID 6f4t

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