9d5z: Difference between revisions

Latest revision as of 14:53, 19 February 2025

Crystal structure of the human WDR5 in complex with LH168 compound

Structural highlights

9d5z is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	A1A16, EDO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

WDR5_HUMAN Contributes to histone modification. May position the N-terminus of histone H3 for efficient trimethylation at 'Lys-4'. As part of the MLL1/MLL complex it is involved in methylation and dimethylation at 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues. May regulate osteoblasts differentiation.^[1] ^[2] ^[3] ^[4] ^[5]

References

↑ Patel A, Dharmarajan V, Vought VE, Cosgrove MS. On the mechanism of multiple lysine methylation by the human mixed lineage leukemia protein-1 (MLL1) core complex. J Biol Chem. 2009 Sep 4;284(36):24242-56. Epub 2009 Jun 25. PMID:19556245 doi:M109.014498
↑ Guelman S, Kozuka K, Mao Y, Pham V, Solloway MJ, Wang J, Wu J, Lill JR, Zha J. The double-histone-acetyltransferase complex ATAC is essential for mammalian development. Mol Cell Biol. 2009 Mar;29(5):1176-88. doi: 10.1128/MCB.01599-08. Epub 2008 Dec, 22. PMID:19103755 doi:10.1128/MCB.01599-08
↑ Cai Y, Jin J, Swanson SK, Cole MD, Choi SH, Florens L, Washburn MP, Conaway JW, Conaway RC. Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. J Biol Chem. 2010 Feb 12;285(7):4268-72. doi: 10.1074/jbc.C109.087981. Epub 2009 , Dec 14. PMID:20018852 doi:10.1074/jbc.C109.087981
↑ Han Z, Guo L, Wang H, Shen Y, Deng XW, Chai J. Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell. 2006 Apr 7;22(1):137-44. PMID:16600877 doi:10.1016/j.molcel.2006.03.018
↑ Couture JF, Collazo E, Trievel RC. Molecular recognition of histone H3 by the WD40 protein WDR5. Nat Struct Mol Biol. 2006 Aug;13(8):698-703. Epub 2006 Jul 9. PMID:16829960 doi:10.1038/nsmb1116

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OCA

[1] Patel A, Dharmarajan V, Vought VE, Cosgrove MS. On the mechanism of multiple lysine methylation by the human mixed lineage leukemia protein-1 (MLL1) core complex. J Biol Chem. 2009 Sep 4;284(36):24242-56. Epub 2009 Jun 25. PMID:19556245 doi:M109.014498

[2] Guelman S, Kozuka K, Mao Y, Pham V, Solloway MJ, Wang J, Wu J, Lill JR, Zha J. The double-histone-acetyltransferase complex ATAC is essential for mammalian development. Mol Cell Biol. 2009 Mar;29(5):1176-88. doi: 10.1128/MCB.01599-08. Epub 2008 Dec, 22. PMID:19103755 doi:10.1128/MCB.01599-08

[3] Cai Y, Jin J, Swanson SK, Cole MD, Choi SH, Florens L, Washburn MP, Conaway JW, Conaway RC. Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. J Biol Chem. 2010 Feb 12;285(7):4268-72. doi: 10.1074/jbc.C109.087981. Epub 2009 , Dec 14. PMID:20018852 doi:10.1074/jbc.C109.087981

[4] Han Z, Guo L, Wang H, Shen Y, Deng XW, Chai J. Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell. 2006 Apr 7;22(1):137-44. PMID:16600877 doi:10.1016/j.molcel.2006.03.018

[5] Couture JF, Collazo E, Trievel RC. Molecular recognition of histone H3 by the WD40 protein WDR5. Nat Struct Mol Biol. 2006 Aug;13(8):698-703. Epub 2006 Jul 9. PMID:16829960 doi:10.1038/nsmb1116

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9d5z is ON HOLD
+==Crystal structure of the human WDR5 in complex with LH168 compound==
+<StructureSection load='9d5z' size='340' side='right'caption='[[9d5z]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-Authors: Kimani, S., Dong, A., Hoffmann, L., Nemec, V., Ackloo, S., Muller-Knapp, S., Knapp, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9d5z]] 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=9D5Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9D5Z FirstGlance]. <br>
-Description: Crystal structure of the human WDR5 in complex with LH168 compound
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1A16:~{N}-[(2~{S})-1-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-yl)-1-oxidanylidene-pentan-2-yl]-3-[1-ethyl-3-(trifluoromethyl)pyrazol-4-yl]-5-(imidazol-1-ylmethyl)benzamide'>A1A16</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-[[Category: Arrowsmith, C.H]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9d5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9d5z OCA], [https://pdbe.org/9d5z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9d5z RCSB], [https://www.ebi.ac.uk/pdbsum/9d5z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9d5z ProSAT]</span></td></tr>
-[[Category: Knapp, S]]
+</table>
-[[Category: Ackloo, S]]
+== Function ==
-[[Category: Structural Genomics Consortium (Sgc)]]
+[https://www.uniprot.org/uniprot/WDR5_HUMAN WDR5_HUMAN] Contributes to histone modification. May position the N-terminus of histone H3 for efficient trimethylation at 'Lys-4'. As part of the MLL1/MLL complex it is involved in methylation and dimethylation at 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues. May regulate osteoblasts differentiation.<ref>PMID:19556245</ref> <ref>PMID:19103755</ref> <ref>PMID:20018852</ref> <ref>PMID:16600877</ref> <ref>PMID:16829960</ref>
-[[Category: Muller-Knapp, S]]
+== References ==
-[[Category: Edwards, A.M]]
+<references/>
-[[Category: Halabelian, L]]
+__TOC__
-[[Category: Dong, A]]
+</StructureSection>
-[[Category: Kimani, S]]
+[[Category: Homo sapiens]]
-[[Category: Hoffmann, L]]
+[[Category: Large Structures]]
-[[Category: Nemec, V]]
+[[Category: Ackloo S]]
+[[Category: Arrowsmith CH]]
+[[Category: Dong A]]
+[[Category: Edwards AM]]
+[[Category: Halabelian L]]
+[[Category: Hoffmann L]]
+[[Category: Kimani S]]
+[[Category: Knapp S]]
+[[Category: Muller-Knapp S]]
+[[Category: Nemec V]]

9d5z: Difference between revisions

Latest revision as of 14:53, 19 February 2025

Crystal structure of the human WDR5 in complex with LH168 compound

Structural highlights

Function

References

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