5yiz - Revision history

OCA at 08:31, 22 November 2023

OCA — Wed, 22 Nov 2023 08:31:43 GMT

←Older revision		Revision as of 08:31, 22 November 2023
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	==Mouse Cereblon thalidomide binding domain complexed with racemic thalidomide==		==Mouse Cereblon thalidomide binding domain complexed with racemic thalidomide==
-	<StructureSection load='5yiz' size='340' side='right' caption='[[5yiz]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5yiz' size='340' side='right'caption='[[5yiz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yiz]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YIZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yiz]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YIZ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EF2:S~~-~~THALIDOMIDE'>EF2</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[3wx2\|3wx2]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Crbn ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])~~</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5yiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yiz OCA], [https://pdbe.org/5yiz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yiz RCSB], [https://www.ebi.ac.uk/pdbsum/5yiz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yiz ProSAT]</span></td></tr>
-	<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=5yiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yiz OCA], [~~http~~://pdbe.org/5yiz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yiz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yiz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yiz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CRBN_MOUSE CRBN_MOUSE]] Component of some DCX (DDB1-CUL4-X-box) E3 protein ligase complex, a complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins and is required for limb outgrowth and expression of the fibroblast growth factor FGF8. In the complex, may act as a substrate receptor. Regulates the assembly and neuronal surface expression of large-conductance calcium-activated potassium channels in brain regions involved in memory and learning via its interaction with KCNT1 (By similarity).	+	[https://www.uniprot.org/uniprot/CRBN_MOUSE CRBN_MOUSE] Component of some DCX (DDB1-CUL4-X-box) E3 protein ligase complex, a complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins and is required for limb outgrowth and expression of the fibroblast growth factor FGF8. In the complex, may act as a substrate receptor. Regulates the assembly and neuronal surface expression of large-conductance calcium-activated potassium channels in brain regions involved in memory and learning via its interaction with KCNT1 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5yiz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yiz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Hakoshima, T~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Mori,~~ T]]	+	[[Category: Hakoshima T]]
-	[[Category: ~~Metal binding protein]]~~	+	[[Category: Mori T]]
-	~~[[Category: Zinc binding protein~~]]	+

OCA at 07:01, 15 February 2018

OCA — Thu, 15 Feb 2018 07:01:53 GMT

←Older revision		Revision as of 07:01, 15 February 2018
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-	==Mouse Cereblon ~~Racemic form~~==	+	==Mouse Cereblon thalidomide binding domain complexed with racemic thalidomide==
	<StructureSection load='5yiz' size='340' side='right' caption='[[5yiz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5yiz' size='340' side='right' caption='[[5yiz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yiz]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yiz]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wx2\|3wx2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wx2\|3wx2]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Crbn ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
	<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=5yiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yiz OCA], [http://pdbe.org/5yiz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yiz RCSB], [http://www.ebi.ac.uk/pdbsum/5yiz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yiz ProSAT]</span></td></tr>		<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=5yiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yiz OCA], [http://pdbe.org/5yiz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yiz RCSB], [http://www.ebi.ac.uk/pdbsum/5yiz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yiz ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Hakoshima, T]]		[[Category: Hakoshima, T]]
	[[Category: Mori, T]]		[[Category: Mori, T]]
	[[Category: Metal binding protein]]		[[Category: Metal binding protein]]
	[[Category: Zinc binding protein]]		[[Category: Zinc binding protein]]

OCA at 06:16, 7 February 2018

OCA — Wed, 07 Feb 2018 06:16:35 GMT

←Older revision		Revision as of 06:16, 7 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yiz is ~~ON HOLD until Oct 06 2019~~	+	==Mouse Cereblon Racemic form==
		+	<StructureSection load='5yiz' size='340' side='right' caption='[[5yiz]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yiz]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wx2\|3wx2]]</td></tr>
		+	<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=5yiz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yiz OCA], [http://pdbe.org/5yiz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yiz RCSB], [http://www.ebi.ac.uk/pdbsum/5yiz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yiz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CRBN_MOUSE CRBN_MOUSE]] Component of some DCX (DDB1-CUL4-X-box) E3 protein ligase complex, a complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins and is required for limb outgrowth and expression of the fibroblast growth factor FGF8. In the complex, may act as a substrate receptor. Regulates the assembly and neuronal surface expression of large-conductance calcium-activated potassium channels in brain regions involved in memory and learning via its interaction with KCNT1 (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Thalidomide possesses two optical isomers which have been reported to exhibit different pharmacological and toxicological activities. However, the precise mechanism by which the two isomers exert their different activities remains poorly understood. Here, we present structural and biochemical studies of (S)- and (R)-enantiomers bound to the primary target of thalidomide, cereblon (CRBN). Our biochemical studies employed deuterium-substituted thalidomides to suppress optical isomer conversion, and established that the (S)-enantiomer exhibited ~10-fold stronger binding to CRBN and inhibition of self-ubiquitylation compared to the (R)-enantiomer. The crystal structures of the thalidomide-binding domain of CRBN bound to each enantiomer show that both enantiomers bind the tri-Trp pocket, although the bound form of the (S)-enantiomer exhibited a more relaxed glutarimide ring conformation. The (S)-enantiomer induced greater teratogenic effects on fins of zebrafish compared to the (R)-enantiomer. This study has established a mechanism by which thalidomide exerts its effects in a stereospecific manner at the atomic level.

-	~~Authors~~:	+	Structural basis of thalidomide enantiomer binding to cereblon.,Mori T, Ito T, Liu S, Ando H, Sakamoto S, Yamaguchi Y, Tokunaga E, Shibata N, Handa H, Hakoshima T Sci Rep. 2018 Jan 22;8(1):1294. doi: 10.1038/s41598-018-19202-7. PMID:29358579<ref>PMID:29358579</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yiz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hakoshima, T]]
		+	[[Category: Mori, T]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Zinc binding protein]]

OCA: Protected "5yiz" [edit=sysop:move=sysop]

OCA — Wed, 25 Oct 2017 05:36:14 GMT

Protected "5yiz" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:36, 25 October 2017

OCA: New page: '''Unreleased structure''' The entry 5yiz is ON HOLD until Oct 06 2019 Authors: Description: Category: Unreleased Structures

OCA — Wed, 25 Oct 2017 05:36:13 GMT

New page: '''Unreleased structure''' The entry 5yiz is ON HOLD until Oct 06 2019 Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yiz is ON HOLD until Oct 06 2019

Authors:

Description:
[[Category: Unreleased Structures]]