6lxd - Revision history

OCA at 10:47, 27 March 2024

OCA — Wed, 27 Mar 2024 10:47:47 GMT

←Older revision		Revision as of 10:47, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6lxd' size='340' side='right'caption='[[6lxd]], [[Resolution\|resolution]] 3.90Å' scene=''>		<StructureSection load='6lxd' size='340' side='right'caption='[[6lxd]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lxd]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LXD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6LXD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lxd]] is a 4 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=6LXD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LXD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 3.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DROSHA, RN3, RNASE3L, RNASEN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), DGCR8, C22orf12, DGCRK6, LP4941 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3]~~ </~~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=6lxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lxd OCA], [https://pdbe.org/6lxd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lxd RCSB], [https://www.ebi.ac.uk/pdbsum/6lxd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lxd 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=6lxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lxd OCA], [~~http~~://pdbe.org/6lxd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6lxd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6lxd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6lxd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RNC_HUMAN RNC_HUMAN]] Ribonuclease III double-stranded (ds) RNA-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. Component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, DROSHA cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. Involved also in pre-rRNA processing. Cleaves double-strand RNA and does not cleave single-strand RNA. Involved in the formation of GW bodies.<ref>PMID:10948199</ref> <ref>PMID:14508493</ref> <ref>PMID:15589161</ref> <ref>PMID:15574589</ref> <ref>PMID:15531877</ref> <ref>PMID:15565168</ref> <ref>PMID:16751099</ref> <ref>PMID:16906129</ref> <ref>PMID:17159994</ref> [[http://www.uniprot.org/uniprot/DGCR8_HUMAN DGCR8_HUMAN]] Component of the microprocessor complex that acts as a RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, DGCR8 function as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11 bp away form the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. The heme-bound DGCR8 dimer binds pri-miRNAs as a cooperative trimer (of dimers) and is active in triggering pri-miRNA cleavage, whereas the heme-free DGCR8 monomer binds pri-miRNAs as a dimer and is much less active. Both double-stranded and single-stranded regions of a pri-miRNA are required for its binding. Involved in the silencing of embryonic stem cells self-renewal.<ref>PMID:15589161</ref> <ref>PMID:15574589</ref> <ref>PMID:15531877</ref> <ref>PMID:16751099</ref> <ref>PMID:16906129</ref> <ref>PMID:16963499</ref> <ref>PMID:17159994</ref>	+	[https://www.uniprot.org/uniprot/RNC_HUMAN RNC_HUMAN] Ribonuclease III double-stranded (ds) RNA-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. Component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, DROSHA cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. Involved also in pre-rRNA processing. Cleaves double-strand RNA and does not cleave single-strand RNA. Involved in the formation of GW bodies.<ref>PMID:10948199</ref> <ref>PMID:14508493</ref> <ref>PMID:15589161</ref> <ref>PMID:15574589</ref> <ref>PMID:15531877</ref> <ref>PMID:15565168</ref> <ref>PMID:16751099</ref> <ref>PMID:16906129</ref> <ref>PMID:17159994</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	A commencing and critical step in miRNA biogenesis involves processing of pri-miRNAs in the nucleus by Microprocessor. An important, but not completely understood, question is how Drosha, the catalytic subunit of Microprocessor, binds pri-miRNAs and correctly specifies cleavage sites. Here we report the cryoelectron microscopy structures of the Drosha-DGCR8 complex with and without a pri-miRNA. The RNA-bound structure provides direct visualization of the tertiary structure of pri-miRNA and shows that a helix hairpin in the extended PAZ domain and the mobile basic (MB) helix in the RNase IIIa domain of Drosha coordinate to recognize the single-stranded to double-stranded junction of RNA, whereas the dsRNA binding domain makes extensive contacts with the RNA stem. Furthermore, the RNA-free structure reveals an autoinhibitory conformation of the PAZ helix hairpin. These findings provide mechanistic insights into pri-miRNA cleavage site selection and conformational dynamics governing pri-miRNA recognition by the catalytic component of Microprocessor.	+
-		+
-	Structural Basis for pri-miRNA Recognition by Drosha.,Jin W, Wang J, Liu CP, Wang HW, Xu RM Mol Cell. 2020 Mar 25. pii: S1097-2765(20)30144-1. doi:, 10.1016/j.molcel.2020.02.024. PMID:32220645<ref>PMID:32220645</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6lxd" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ribonuclease III]]~~	+	[[Category: Jin W]]
-	[[Category: Jin, W]]	+	[[Category: Liu CP]]
-	[[Category: Liu~~, C P~~]]	+	[[Category: Wang HW]]
-	[[Category: Wang~~, H W~~]]	+	[[Category: Wang J]]
-	[[Category: Wang, J]]	+	[[Category: Xu RM]]
-	[[Category: Xu~~, R M]]~~	+
-	~~[[Category: Hydrolase-rna binding protein-rna complex]]~~	+
-	~~[[Category: Ribonuclease]]~~	+
-	~~[[Category: Rna binding protein~~]]	+

OCA at 07:16, 27 May 2020

OCA — Wed, 27 May 2020 07:16:41 GMT

←Older revision		Revision as of 07:16, 27 May 2020
Line 1:		Line 1:

	==Pri-miRNA bound DROSHA-DGCR8 complex==		==Pri-miRNA bound DROSHA-DGCR8 complex==
-	<StructureSection load='6lxd' size='340' side='right'caption='[[6lxd]]' scene=''>	+	<StructureSection load='6lxd' size='340' side='right'caption='[[6lxd]], [[Resolution\|resolution]] 3.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LXD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LXD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lxd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LXD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LXD FirstGlance]. <br>
-	</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=6lxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lxd OCA], [http://pdbe.org/6lxd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lxd RCSB], [http://www.ebi.ac.uk/pdbsum/6lxd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lxd ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DROSHA, RN3, RNASE3L, RNASEN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DGCR8, C22orf12, DGCRK6, LP4941 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] </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=6lxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lxd OCA], [http://pdbe.org/6lxd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lxd RCSB], [http://www.ebi.ac.uk/pdbsum/6lxd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lxd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNC_HUMAN RNC_HUMAN]] Ribonuclease III double-stranded (ds) RNA-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. Component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, DROSHA cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. Involved also in pre-rRNA processing. Cleaves double-strand RNA and does not cleave single-strand RNA. Involved in the formation of GW bodies.<ref>PMID:10948199</ref> <ref>PMID:14508493</ref> <ref>PMID:15589161</ref> <ref>PMID:15574589</ref> <ref>PMID:15531877</ref> <ref>PMID:15565168</ref> <ref>PMID:16751099</ref> <ref>PMID:16906129</ref> <ref>PMID:17159994</ref> [[http://www.uniprot.org/uniprot/DGCR8_HUMAN DGCR8_HUMAN]] Component of the microprocessor complex that acts as a RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, DGCR8 function as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11 bp away form the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. The heme-bound DGCR8 dimer binds pri-miRNAs as a cooperative trimer (of dimers) and is active in triggering pri-miRNA cleavage, whereas the heme-free DGCR8 monomer binds pri-miRNAs as a dimer and is much less active. Both double-stranded and single-stranded regions of a pri-miRNA are required for its binding. Involved in the silencing of embryonic stem cells self-renewal.<ref>PMID:15589161</ref> <ref>PMID:15574589</ref> <ref>PMID:15531877</ref> <ref>PMID:16751099</ref> <ref>PMID:16906129</ref> <ref>PMID:16963499</ref> <ref>PMID:17159994</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A commencing and critical step in miRNA biogenesis involves processing of pri-miRNAs in the nucleus by Microprocessor. An important, but not completely understood, question is how Drosha, the catalytic subunit of Microprocessor, binds pri-miRNAs and correctly specifies cleavage sites. Here we report the cryoelectron microscopy structures of the Drosha-DGCR8 complex with and without a pri-miRNA. The RNA-bound structure provides direct visualization of the tertiary structure of pri-miRNA and shows that a helix hairpin in the extended PAZ domain and the mobile basic (MB) helix in the RNase IIIa domain of Drosha coordinate to recognize the single-stranded to double-stranded junction of RNA, whereas the dsRNA binding domain makes extensive contacts with the RNA stem. Furthermore, the RNA-free structure reveals an autoinhibitory conformation of the PAZ helix hairpin. These findings provide mechanistic insights into pri-miRNA cleavage site selection and conformational dynamics governing pri-miRNA recognition by the catalytic component of Microprocessor.
		+
		+	Structural Basis for pri-miRNA Recognition by Drosha.,Jin W, Wang J, Liu CP, Wang HW, Xu RM Mol Cell. 2020 Mar 25. pii: S1097-2765(20)30144-1. doi:, 10.1016/j.molcel.2020.02.024. PMID:32220645<ref>PMID:32220645</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6lxd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jin W]]	+	[[Category: Ribonuclease III]]
-	[[Category: Liu CP]]	+	[[Category: Jin, W]]
-	[[Category: Wang HW]]	+	[[Category: Liu, C P]]
-	[[Category: Wang J]]	+	[[Category: Wang, H W]]
-	[[Category: Xu RM]]	+	[[Category: Wang, J]]
		+	[[Category: Xu, R M]]
		+	[[Category: Hydrolase-rna binding protein-rna complex]]
		+	[[Category: Ribonuclease]]
		+	[[Category: Rna binding protein]]

OCA at 06:52, 15 April 2020

OCA — Wed, 15 Apr 2020 06:52:28 GMT

←Older revision		Revision as of 06:52, 15 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6lxd is ~~ON HOLD until Paper Publication~~	+	==Pri-miRNA bound DROSHA-DGCR8 complex==
-		+	<StructureSection load='6lxd' size='340' side='right'caption='[[6lxd]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LXD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LXD FirstGlance]. <br>
-	~~Description~~:	+	</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=6lxd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lxd OCA], [http://pdbe.org/6lxd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lxd RCSB], [http://www.ebi.ac.uk/pdbsum/6lxd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lxd ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Jin W]]
		+	[[Category: Liu CP]]
		+	[[Category: Wang HW]]
		+	[[Category: Wang J]]
		+	[[Category: Xu RM]]

OCA at 05:27, 8 April 2020

OCA — Wed, 08 Apr 2020 05:27:40 GMT

←Older revision		Revision as of 05:27, 8 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6lxd is ON HOLD	+	The entry 6lxd is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 19 Feb 2020 05:10:21 GMT

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

←Older revision

Revision as of 05:10, 19 February 2020

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

OCA — Wed, 19 Feb 2020 05:10:20 GMT

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

New page

'''Unreleased structure'''

The entry 6lxd is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]