5vjx - Revision history

OCA at 09:36, 1 January 2020

OCA — Wed, 01 Jan 2020 09:36:13 GMT

←Older revision		Revision as of 09:36, 1 January 2020
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	==Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor==		==Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor==
-	<StructureSection load='5vjx' size='340' side='right' caption='[[5vjx]], [[Resolution\|resolution]] 2.69Å' scene=''>	+	<StructureSection load='5vjx' size='340' side='right'caption='[[5vjx]], [[Resolution\|resolution]] 2.69Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vjx]] is a 30 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vjx]] is a 30 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=5VJX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJX FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cipc, Kiaa1737 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), Clock ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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=5vjx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjx OCA], [http://pdbe.org/5vjx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjx RCSB], [http://www.ebi.ac.uk/pdbsum/5vjx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjx 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=5vjx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjx OCA], [http://pdbe.org/5vjx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjx RCSB], [http://www.ebi.ac.uk/pdbsum/5vjx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjx ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Histone acetyltransferase]]		[[Category: Histone acetyltransferase]]
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Grishin, N V]]		[[Category: Grishin, N V]]
	[[Category: Hou, Z]]		[[Category: Hou, Z]]

OCA at 07:15, 6 December 2017

OCA — Wed, 06 Dec 2017 07:15:20 GMT

←Older revision		Revision as of 07:15, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vjx is ~~ON HOLD~~	+	==Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor==
		+	<StructureSection load='5vjx' size='340' side='right' caption='[[5vjx]], [[Resolution\|resolution]] 2.69Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vjx]] is a 30 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJX FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </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=5vjx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vjx OCA], [http://pdbe.org/5vjx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vjx RCSB], [http://www.ebi.ac.uk/pdbsum/5vjx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vjx ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CIPC_MOUSE CIPC_MOUSE]] Transcriptional repressor which may act as a negative-feedback regulator of CLOCK-ARNTL/BMAL1 transcriptional activity in the circadian-clock mechanism. May stimulate ARNTL/BMAL1-dependent phosphorylation of CLOCK (PubMed:17310242, PubMed:19414601). However, the physiogical relevance of these observations is unsure, since experiments in knockout mice showed that CIPC is not critially required for basic circadian clock (PubMed:25862660).<ref>PMID:17310242</ref> <ref>PMID:19414601</ref> <ref>PMID:25862660</ref> [[http://www.uniprot.org/uniprot/CLOCK_MOUSE CLOCK_MOUSE]] Transcriptional activator which forms a core component of the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers'). The predominant Zeitgeber for the central clock is light, which is sensed by retina and signals directly to the SCN. The central clock entrains the peripheral clocks through neuronal and hormonal signals, body temperature and feeding-related cues, aligning all clocks with the external light/dark cycle. Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating gene expression to create a peak of protein expression once every 24 hours to control when a particular physiological process is most active with respect to the solar day. Transcription and translation of core clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2, PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythm generation, whereas delays imposed by post-translational modifications (PTMs) are important for determining the period (tau) of the rhythms (tau refers to the period of a rhythm and is the length, in time, of one complete cycle). A diurnal rhythm is synchronized with the day/night cycle, while the ultradian and infradian rhythms have a period shorter and longer than 24 hours, respectively. Disruptions in the circadian rhythms contribute to the pathology of cardiovascular diseases, cancer, metabolic syndromes and aging. A transcription/translation feedback loop (TTFL) forms the core of the molecular circadian clock mechanism. Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 or ARNTL2/BMAL2, form the positive limb of the feedback loop, act in the form of a heterodimer and activate the transcription of core clock genes and clock-controlled genes (involved in key metabolic processes), harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are transcriptional repressors form the negative limb of the feedback loop and interact with the CLOCK\|NPAS2-ARNTL/BMAL1\|ARNTL2/BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression. This heterodimer also activates nuclear receptors NR1D1/2 and RORA/B/G, which form a second feedback loop and which activate and repress ARNTL/BMAL1 transcription, respectively. CLOCK has an intrinsic acetyltransferase activity, which enables circadian chromatin remodeling by acetylating histones and nonhistone proteins, including its own partner ARNTL/BMAL1. Regulates the circadian expression of ICAM1, VCAM1, CCL2, THPO and MPL and also acts as an enhancer of the transactivation potential of NF-kappaB. Plays an important role in the homeostatic regulation of sleep. The CLOCK-ARNTL/BMAL1 heterodimer regulates the circadian expression of SERPINE1/PAI1, VWF, B3, CCRN4L/NOC, NAMPT, DBP, MYOD1, PPARGC1A, PPARGC1B, SIRT1, GYS2, F7, NGFR, GNRHR, BHLHE40/DEC1, ATF4, MTA1, KLF10 and also genes implicated in glucose and lipid metabolism. Represses glucocorticoid receptor NR3C1/GR-induced transcriptional activity by reducing the association of NR3C1/GR to glucocorticoid response elements (GREs) via the acetylation of multiple lysine residues located in its hinge region. Promotes rhythmic chromatin opening, regulating the DNA accessibility of other transcription factors. May play a role in spermatogenesis; contributes to the chromatoid body assembly and physiology. The CLOCK-ARNTL2/BMAL2 heterodimer activates the transcription of SERPINE1/PAI1 and BHLHE40/DEC1.<ref>PMID:12738229</ref> <ref>PMID:14672706</ref> <ref>PMID:16678094</ref> <ref>PMID:17417633</ref> <ref>PMID:18075593</ref> <ref>PMID:18316400</ref> <ref>PMID:19141540</ref> <ref>PMID:19286518</ref> <ref>PMID:19299583</ref> <ref>PMID:19605937</ref> <ref>PMID:20385766</ref> <ref>PMID:20430893</ref> <ref>PMID:20562852</ref> <ref>PMID:20658528</ref> <ref>PMID:20956306</ref> <ref>PMID:21768648</ref> <ref>PMID:22284746</ref> <ref>PMID:22653727</ref> <ref>PMID:22895791</ref> <ref>PMID:22900038</ref> <ref>PMID:22981862</ref> <ref>PMID:23291174</ref> <ref>PMID:23785138</ref> <ref>PMID:24089055</ref> <ref>PMID:24270424</ref> <ref>PMID:24333415</ref> <ref>PMID:24378737</ref> <ref>PMID:24385426</ref> <ref>PMID:24395244</ref> <ref>PMID:24442997</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In the canonical clock model, CLOCK:BMAL1-mediated transcriptional activation is feedback regulated by its repressors CRY and PER and, in association with other coregulators, ultimately generates oscillatory gene expression patterns. How CLOCK:BMAL1 interacts with coregulator(s) is not well understood. Here we report the crystal structures of the mouse CLOCK transactivating domain Exon19 in complex with CIPC, a potent circadian repressor that functions independently of CRY and PER. The Exon19:CIPC complex adopts a three-helical coiled-coil bundle conformation containing two Exon19 helices and one CIPC. Unique to Exon19:CIPC, three highly conserved polar residues, Asn341 of CIPC and Gln544 of the two Exon19 helices, are located at the mid-section of the coiled-coil bundle interior and form hydrogen bonds with each other. Combining results from protein database search, sequence analysis, and mutagenesis studies, we discovered for the first time that CLOCK Exon19:CIPC interaction is a conserved transcription regulatory mechanism among mammals, fish, flies, and other invertebrates.

-	~~Authors: Hou~~, Z., Su, L., Pei, J., Grishin, N.V., ~~Zhang, H~~.	+	Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor.,Hou Z, Su L, Pei J, Grishin NV, Zhang H Structure. 2017 Aug 1;25(8):1187-1194.e3. doi: 10.1016/j.str.2017.05.023. Epub, 2017 Jun 29. PMID:28669630<ref>PMID:28669630</ref>

-	~~Description: Crystal structure~~ of the ~~CLOCK Transcription Domain Exon19 in Complex with a Repressor~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Zhang, H~~]]	+	<div class="pdbe-citations 5vjx" style="background-color:#fffaf0;"></div>
-	[[Category: Grishin, N.V]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Histone acetyltransferase]]
		+	[[Category: Grishin, N V]]
	[[Category: Hou, Z]]		[[Category: Hou, Z]]
	[[Category: Pei, J]]		[[Category: Pei, J]]
	[[Category: Su, L]]		[[Category: Su, L]]
		+	[[Category: Zhang, H]]
		+	[[Category: Cipc]]
		+	[[Category: Circadian clock]]
		+	[[Category: Circadian rhythm]]
		+	[[Category: Clock protein]]
		+	[[Category: Coiled coil]]
		+	[[Category: Repressor]]
		+	[[Category: Transcription activation]]
		+	[[Category: Transferase]]

OCA at 14:05, 27 September 2017

OCA — Wed, 27 Sep 2017 14:05:07 GMT

←Older revision		Revision as of 14:05, 27 September 2017
Line 9:		Line 9:
	[[Category: Zhang, H]]		[[Category: Zhang, H]]
	[[Category: Grishin, N.V]]		[[Category: Grishin, N.V]]
-	[[Category: Su, L]]
	[[Category: Hou, Z]]		[[Category: Hou, Z]]
	[[Category: Pei, J]]		[[Category: Pei, J]]
		+	[[Category: Su, L]]

OCA at 11:23, 4 May 2017

OCA — Thu, 04 May 2017 11:23:17 GMT

←Older revision		Revision as of 11:23, 4 May 2017
Line 3:		Line 3:
	The entry 5vjx is ON HOLD		The entry 5vjx is ON HOLD

-	Authors: ~~Zhiqiang~~ Hou, ~~Lijing~~ Su, ~~Jimin~~ Pei, ~~Nick V~~. Grishin, ~~Hong~~ Zhang	+	Authors: Hou, Z., Su, L., Pei, J., Grishin, N.V., Zhang, H.

	Description: Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor		Description: Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Zhiqiang Hou~~, ~~Lijing~~ Su, ~~Jimin~~ Pei, ~~Nick V. Grishin, Hong Zhang~~]]	+	[[Category: Zhang, H]]
		+	[[Category: Grishin, N.V]]
		+	[[Category: Su, L]]
		+	[[Category: Hou, Z]]
		+	[[Category: Pei, J]]

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

OCA — Thu, 27 Apr 2017 12:22:37 GMT

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

←Older revision

Revision as of 12:22, 27 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vjx is ON HOLD Authors: Zhiqiang Hou, Lijing Su, Jimin Pei, Nick V. Grishin, Hong Zhang Description: Crystal structure of the CLOCK Transcription ...

OCA — Thu, 27 Apr 2017 12:22:36 GMT

New page: '''Unreleased structure''' The entry 5vjx is ON HOLD Authors: Zhiqiang Hou, Lijing Su, Jimin Pei, Nick V. Grishin, Hong Zhang Description: Crystal structure of the CLOCK Transcription ...

New page

'''Unreleased structure'''

The entry 5vjx is ON HOLD

Authors: Zhiqiang Hou, Lijing Su, Jimin Pei, Nick V. Grishin, Hong Zhang

Description: Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor
[[Category: Unreleased Structures]]
[[Category: Zhiqiang Hou, Lijing Su, Jimin Pei, Nick V. Grishin, Hong Zhang]]