6j4z - Revision history

OCA at 10:36, 27 March 2024

OCA — Wed, 27 Mar 2024 10:36:45 GMT

←Older revision		Revision as of 10:36, 27 March 2024
Line 3:		Line 3:
	<SX load='6j4z' size='340' side='right' viewer='molstar' caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>		<SX load='6j4z' size='340' side='right' viewer='molstar' caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc~~] and [~~http~~://en.wikipedia.org/wiki/~~Kompg Kompg~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j4z]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Komagataella_phaffii_CBS_7435 Komagataella phaffii CBS 7435] and [https://en.wikipedia.org/wiki/Komagataella_phaffii_GS115 Komagataella phaffii GS115]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">Electron Microscopy, [[Resolution\|Resolution]] 4.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PAS_chr2-1_0350 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=644223 KOMPG]), H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2BJ, H2BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG])</td><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6]~~ </~~span~~></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=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [https://pdbe.org/6j4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [https://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [~~http~~://pdbe.org/6j4z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/H2B1J_HUMAN H2B1J_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref> Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref> [[http://www.uniprot.org/uniprot/C4QZQ7_KOMPG C4QZQ7_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279] [[http://www.uniprot.org/uniprot/C4R0E6_KOMPG C4R0E6_KOMPG]] The SPT4-SPT5 complex mediates both activation and inhibition of transcription elongation, and plays a role in pre-mRNA processing. This complex seems to be important for the stability of the RNA polymerase II elongation machinery on the chromatin template but not for the inherent ability of this machinery to translocate down the gene.[PIRNR:PIRNR025023] [[http://www.uniprot.org/uniprot/F2QPE6_KOMPC F2QPE6_KOMPC]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[PIRNR:PIRNR005586]	+	[https://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.	+
-		+
-	Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.,Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI Science. 2019 Feb 15;363(6428):744-747. doi: 10.1126/science.aav8912. Epub 2019, Feb 7. PMID:30733384<ref>PMID:30733384</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6j4z" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
		+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	*[[Histone 3D structures\|Histone 3D structures]]		*[[Histone 3D structures\|Histone 3D structures]]
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~Atcc 28485~~]]	+	[[Category: Komagataella phaffii CBS 7435]]
-	[[Category: ~~DNA-directed RNA polymerase]]~~	+	[[Category: Komagataella phaffii GS115]]
-	~~[[Category: Kompc]]~~	+
-	~~[[Category: Kompg~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ehara, H]]	+	[[Category: Ehara H]]
-	[[Category: Fujino, Y]]	+	[[Category: Fujino Y]]
-	[[Category: Kujirai, T]]	+	[[Category: Kujirai T]]
-	[[Category: Kurumizaka, H]]	+	[[Category: Kurumizaka H]]
-	[[Category: Sekine, S]]	+	[[Category: Sekine S]]
-	[[Category: Shirouzu, M]]	+	[[Category: Shirouzu M]]
-	~~[[Category: Chromatin]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Rna polymerase]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription-rna-dna complex~~]]	+

OCA at 01:58, 11 April 2020

OCA — Sat, 11 Apr 2020 01:58:57 GMT

←Older revision		Revision as of 01:58, 11 April 2020
Line 3:		Line 3:
	<SX load='6j4z' size='340' side='right' viewer='molstar' caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>		<SX load='6j4z' size='340' side='right' viewer='molstar' caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">PAS_chr2-1_0350 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2BJ, H2BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAS_chr2-1_0350 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2BJ, H2BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [http://pdbe.org/6j4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [http://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [http://pdbe.org/6j4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [http://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 22:13, 6 March 2020

OCA — Fri, 06 Mar 2020 22:13:20 GMT

←Older revision		Revision as of 22:13, 6 March 2020
Line 1:		Line 1:

	==RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome==		==RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome==
-	<~~StructureSection~~ load='6j4z' size='340' side='right'caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>	+	<SX load='6j4z' size='340' side='right' viewer='molstar' caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>
Line 23:		Line 23:
	==See Also==		==See Also==
	*[[Histone 3D structures\|Histone 3D structures]]		*[[Histone 3D structures\|Histone 3D structures]]
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Atcc 28485]]		[[Category: Atcc 28485]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]

OCA at 08:05, 6 November 2019

OCA — Wed, 06 Nov 2019 08:05:28 GMT

←Older revision		Revision as of 08:05, 6 November 2019
Line 1:		Line 1:

	==RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome==		==RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome==
-	<StructureSection load='6j4z' size='340' side='right' caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>	+	<StructureSection load='6j4z' size='340' side='right'caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6j4z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6j4z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone 3D structures\|Histone 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 31:
	[[Category: Kompc]]		[[Category: Kompc]]
	[[Category: Kompg]]		[[Category: Kompg]]
		+	[[Category: Large Structures]]
	[[Category: Ehara, H]]		[[Category: Ehara, H]]
	[[Category: Fujino, Y]]		[[Category: Fujino, Y]]

OCA at 16:05, 27 February 2019

OCA — Wed, 27 Feb 2019 16:05:53 GMT

←Older revision		Revision as of 16:05, 27 February 2019
Line 3:		Line 3:
	<StructureSection load='6j4z' size='340' side='right' caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>		<StructureSection load='6j4z' size='340' side='right' caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/~~Komagataella_phaffii_(strain_atcc_76273_/_cbs_7435_/_cect_11047_/_nrrl_y-11430_/_wegner_21-1) Komagataella phaffii (strain atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner 21-1)~~] and [http://en.wikipedia.org/wiki/~~Komagataella_phaffii_(strain_gs115_/_atcc_20864) Komagataella phaffii (strain gs115 / atcc 20864)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485], [http://en.wikipedia.org/wiki/Kompc Kompc] and [http://en.wikipedia.org/wiki/Kompg Kompg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</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">PAS_chr2-1_0350 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG]), HIST1H2BJ, H2BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=644223 KOMPG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [http://pdbe.org/6j4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [http://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z 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=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [http://pdbe.org/6j4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [http://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z ProSAT]</span></td></tr>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 28485]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Kompc]]
		+	[[Category: Kompg]]
	[[Category: Ehara, H]]		[[Category: Ehara, H]]
	[[Category: Fujino, Y]]		[[Category: Fujino, Y]]

OCA at 06:52, 21 February 2019

OCA — Thu, 21 Feb 2019 06:52:26 GMT

←Older revision		Revision as of 06:52, 21 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6j4z is ~~ON HOLD~~	+	==RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome==
		+	<StructureSection load='6j4z' size='340' side='right' caption='[[6j4z]], [[Resolution\|resolution]] 4.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6j4z]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_atcc_76273_/_cbs_7435_/_cect_11047_/_nrrl_y-11430_/_wegner_21-1) Komagataella phaffii (strain atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner 21-1)] and [http://en.wikipedia.org/wiki/Komagataella_phaffii_(strain_gs115_/_atcc_20864) Komagataella phaffii (strain gs115 / atcc 20864)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J4Z FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </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=6j4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j4z OCA], [http://pdbe.org/6j4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j4z RCSB], [http://www.ebi.ac.uk/pdbsum/6j4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j4z ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/H2B1J_HUMAN H2B1J_HUMAN]] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref> Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref> [[http://www.uniprot.org/uniprot/C4QZQ7_KOMPG C4QZQ7_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/C4R4Y0_KOMPG C4R4Y0_KOMPG]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU004279] [[http://www.uniprot.org/uniprot/C4R0E6_KOMPG C4R0E6_KOMPG]] The SPT4-SPT5 complex mediates both activation and inhibition of transcription elongation, and plays a role in pre-mRNA processing. This complex seems to be important for the stability of the RNA polymerase II elongation machinery on the chromatin template but not for the inherent ability of this machinery to translocate down the gene.[PIRNR:PIRNR025023] [[http://www.uniprot.org/uniprot/F2QPE6_KOMPC F2QPE6_KOMPC]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[PIRNR:PIRNR005586]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.

-	~~Authors~~:	+	Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.,Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI Science. 2019 Feb 15;363(6428):744-747. doi: 10.1126/science.aav8912. Epub 2019, Feb 7. PMID:30733384<ref>PMID:30733384</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6j4z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Ehara, H]]
		+	[[Category: Fujino, Y]]
		+	[[Category: Kujirai, T]]
		+	[[Category: Kurumizaka, H]]
		+	[[Category: Sekine, S]]
		+	[[Category: Shirouzu, M]]
		+	[[Category: Chromatin]]
		+	[[Category: Nucleosome]]
		+	[[Category: Rna polymerase]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription-rna-dna complex]]

OCA: Protected "6j4z" [edit=sysop:move=sysop]

OCA — Wed, 16 Jan 2019 10:27:51 GMT

Protected "6j4z" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:27, 16 January 2019

OCA: New page: '''Unreleased structure''' The entry 6j4z is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 16 Jan 2019 10:27:49 GMT

New page: '''Unreleased structure''' The entry 6j4z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6j4z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]