7prd - Revision history

OCA at 06:16, 19 June 2024

2024-06-19T06:16:19Z

← Older revision		Revision as of 06:16, 19 June 2024
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	<StructureSection load='7prd' size='340' side='right'caption='[[7prd]]' scene=''>		<StructureSection load='7prd' size='340' side='right'caption='[[7prd]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7prd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae].~~ Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PRD FirstGlance]. <br>		<table><tr><td colspan='2'>Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PRD FirstGlance]. <br>
	</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=7prd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7prd OCA], [https://pdbe.org/7prd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7prd RCSB], [https://www.ebi.ac.uk/pdbsum/7prd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7prd ProSAT]</span></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=7prd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7prd OCA], [https://pdbe.org/7prd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7prd RCSB], [https://www.ebi.ac.uk/pdbsum/7prd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7prd ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[https://www.uniprot.org/uniprot/NRD1_YEAST NRD1_YEAST] Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance.[https://www.uniprot.org/uniprot/NAB3_YEAST NAB3_YEAST] May be required for packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Binds to poly(A)+ RNA. Appears to act in the maintenance of CLN3 mRNA levels.<ref>PMID:7476874</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Heterodimerization of RNA binding proteins Nrd1 and Nab3 is essential to communicate the RNA recognition in the nascent transcript with the Nrd1 recognition of the Ser5-phosphorylated Rbp1 C-terminal domain in RNA polymerase II. The structure of a Nrd1-Nab3 chimera reveals the basis of heterodimerization, filling a missing gap in knowledge of this system. The free form of the Nrd1 interaction domain of Nab3 (NRID) forms a multi-state three-helix bundle that is clamped in a single conformation upon complex formation with the Nab3 interaction domain of Nrd1 (NAID). The latter domain forms two long helices that wrap around NRID, resulting in an extensive protein-protein interface that would explain the highly favorable free energy of heterodimerization. Mutagenesis of some conserved hydrophobic residues involved in the heterodimerization leads to temperature-sensitive phenotypes, revealing the importance of this interaction in yeast cell fitness. The Nrd1-Nab3 structure resembles the previously reported Rna14/Rna15 heterodimer structure, which is part of the poly(A)-dependent termination pathway, suggesting that both machineries use similar structural solutions despite they share little sequence homology and are potentially evolutionary divergent.

	Structural basis of Nrd1-Nab3 heterodimerization.,Chaves-Arquero B, Martinez-Lumbreras S, Camero S, Santiveri CM, Mirassou Y, Campos-Olivas R, Jimenez MA, Calvo O, Perez-Canadillas JM Life Sci Alliance. 2022 Jan 12;5(4). pii: 5/4/e202101252. doi:, 10.26508/lsa.202101252. Print 2022 Apr. PMID:35022249<ref>PMID:35022249</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7prd" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Saccharomyces cerevisiae]]~~
	[[Category: Chaves-Arquero B]]		[[Category: Chaves-Arquero B]]
	[[Category: Martinez-Lumbreras S]]		[[Category: Martinez-Lumbreras S]]
	[[Category: Perez-Canadillas JM]]		[[Category: Perez-Canadillas JM]]

OCA at 11:19, 14 June 2023

2023-06-14T11:19:31Z

← Older revision		Revision as of 11:19, 14 June 2023
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	==Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains==		==Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains==
	<StructureSection load='7prd' size='340' side='right'caption='[[7prd~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>		<StructureSection load='7prd' size='340' side='right'caption='[[7prd]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7prd]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PRD FirstGlance]. <br>		<table><tr><td colspan='2'>[[7prd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PRD FirstGlance]. <br>
	</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=7prd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7prd OCA], [https://pdbe.org/7prd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7prd RCSB], [https://www.ebi.ac.uk/pdbsum/7prd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7prd ProSAT]</span></td></tr>		</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=7prd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7prd OCA], [https://pdbe.org/7prd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7prd RCSB], [https://www.ebi.ac.uk/pdbsum/7prd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7prd ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/NRD1_YEAST NRD1_YEAST] Plays a role in sequence-specific regulation of nuclear pre-mRNA abundance.[https://www.uniprot.org/uniprot/NAB3_YEAST NAB3_YEAST] May be required for packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Binds to poly(A)+ RNA. Appears to act in the maintenance of CLN3 mRNA levels.<ref>PMID:7476874</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chaves-Arquero, B]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Martinez-Lumbreras, S]]		[[Category: Chaves-Arquero B]]
	[[Category: Perez-Canadillas~~, J M]]~~		[[Category: Martinez-Lumbreras S]]
	~~[[Category: Chimera]]~~		[[Category: Perez-Canadillas JM]]
	~~[[Category: Heterodimerization]]~~
	~~[[Category: Nab3]]~~
	~~[[Category: Nns pathway]]~~
	~~[[Category: Nrd1]]~~
	~~[[Category: Transcription]]~~
	~~[[Category: Transcription termination]]~~
	~~[[Category: Yeast~~]]

OCA at 07:11, 27 January 2022

2022-01-27T07:11:10Z

← Older revision		Revision as of 07:11, 27 January 2022
Line 1:		Line 1:

	==Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains==		==Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains==
	<StructureSection load='7prd' size='340' side='right'caption='[[7prd]]' scene=''>		<StructureSection load='7prd' size='340' side='right'caption='[[7prd]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' 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=7PRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PRD FirstGlance]. <br>		<table><tr><td colspan='2'>[[7prd]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PRD FirstGlance]. <br>
	</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=7prd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7prd OCA], [https://pdbe.org/7prd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7prd RCSB], [https://www.ebi.ac.uk/pdbsum/7prd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7prd ProSAT]</span></td></tr>		</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=7prd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7prd OCA], [https://pdbe.org/7prd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7prd RCSB], [https://www.ebi.ac.uk/pdbsum/7prd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7prd ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Heterodimerization of RNA binding proteins Nrd1 and Nab3 is essential to communicate the RNA recognition in the nascent transcript with the Nrd1 recognition of the Ser5-phosphorylated Rbp1 C-terminal domain in RNA polymerase II. The structure of a Nrd1-Nab3 chimera reveals the basis of heterodimerization, filling a missing gap in knowledge of this system. The free form of the Nrd1 interaction domain of Nab3 (NRID) forms a multi-state three-helix bundle that is clamped in a single conformation upon complex formation with the Nab3 interaction domain of Nrd1 (NAID). The latter domain forms two long helices that wrap around NRID, resulting in an extensive protein-protein interface that would explain the highly favorable free energy of heterodimerization. Mutagenesis of some conserved hydrophobic residues involved in the heterodimerization leads to temperature-sensitive phenotypes, revealing the importance of this interaction in yeast cell fitness. The Nrd1-Nab3 structure resembles the previously reported Rna14/Rna15 heterodimer structure, which is part of the poly(A)-dependent termination pathway, suggesting that both machineries use similar structural solutions despite they share little sequence homology and are potentially evolutionary divergent.

			Structural basis of Nrd1-Nab3 heterodimerization.,Chaves-Arquero B, Martinez-Lumbreras S, Camero S, Santiveri CM, Mirassou Y, Campos-Olivas R, Jimenez MA, Calvo O, Perez-Canadillas JM Life Sci Alliance. 2022 Jan 12;5(4). pii: 5/4/e202101252. doi:, 10.26508/lsa.202101252. Print 2022 Apr. PMID:35022249<ref>PMID:35022249</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7prd" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chaves-Arquero B]]		[[Category: Chaves-Arquero, B]]
	[[Category: Martinez-Lumbreras S]]		[[Category: Martinez-Lumbreras, S]]
	[[Category: Perez-Canadillas JM]]		[[Category: Perez-Canadillas, J M]]
			[[Category: Chimera]]
			[[Category: Heterodimerization]]
			[[Category: Nab3]]
			[[Category: Nns pathway]]
			[[Category: Nrd1]]
			[[Category: Transcription]]
			[[Category: Transcription termination]]
			[[Category: Yeast]]

OCA at 09:58, 12 January 2022

2022-01-12T09:58:18Z

← Older revision		Revision as of 09:58, 12 January 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7prd ~~is ON HOLD until Paper Publication~~		==Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains==
			<StructureSection load='7prd' size='340' side='right'caption='[[7prd]]' scene=''>
	~~Authors~~: ~~Chaves~~-~~Arquero~~, B., ~~Martinez-Lumbreras~~, S., ~~Perez-Canadillas~~, J.M.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PRD FirstGlance]. <br>
	~~Description: Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains~~		</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=7prd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7prd OCA], [https://pdbe.org/7prd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7prd RCSB], [https://www.ebi.ac.uk/pdbsum/7prd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7prd ProSAT]</span></td></tr>
	[[Category: ~~Unreleased~~ Structures]]		</table>
	[[Category: ~~Perez~~-~~Canadillas, J.M~~]]		__TOC__
	[[Category: Martinez-Lumbreras, S]]		</StructureSection>
	[[Category: ~~Chaves~~-~~Arquero, B~~]]		[[Category: Large Structures]]
			[[Category: Chaves-Arquero B]]
			[[Category: Martinez-Lumbreras S]]
			[[Category: Perez-Canadillas JM]]

OCA at 14:53, 20 October 2021

2021-10-20T14:53:37Z

← Older revision		Revision as of 14:53, 20 October 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7prd is ON HOLD		The entry 7prd is ON HOLD until Paper Publication

	Authors: Chaves-Arquero, B., Martinez-Lumbreras, S., Perez-Canadillas, J.M.		Authors: Chaves-Arquero, B., Martinez-Lumbreras, S., Perez-Canadillas, J.M.
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	Description: Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains		Description: Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	~~[[Category: Chaves-Arquero, B]]~~
	[[Category: Perez-Canadillas, J.M]]		[[Category: Perez-Canadillas, J.M]]
	[[Category: Martinez-Lumbreras, S]]		[[Category: Martinez-Lumbreras, S]]
			[[Category: Chaves-Arquero, B]]

OCA: Protected "7prd" [edit=sysop:move=sysop]

2021-09-29T07:39:29Z

Protected "7prd" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:39, 29 September 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7prd is ON HOLD Authors: Chaves-Arquero, B., Martinez-Lumbreras, S., Perez-Canadillas, J.M. Description: Solution structure of the chimeric Nrd1-Na...

2021-09-29T07:39:28Z

New page: '''Unreleased structure''' The entry 7prd is ON HOLD Authors: Chaves-Arquero, B., Martinez-Lumbreras, S., Perez-Canadillas, J.M. Description: Solution structure of the chimeric Nrd1-Na...

New page

'''Unreleased structure'''

The entry 7prd is ON HOLD

Authors: Chaves-Arquero, B., Martinez-Lumbreras, S., Perez-Canadillas, J.M.

Description: Solution structure of the chimeric Nrd1-Nab3 heterodimerization domains
[[Category: Unreleased Structures]]
[[Category: Chaves-Arquero, B]]
[[Category: Perez-Canadillas, J.M]]
[[Category: Martinez-Lumbreras, S]]