5f3w - Revision history

OCA at 09:11, 20 March 2024

OCA — Wed, 20 Mar 2024 09:11:43 GMT

←Older revision		Revision as of 09:11, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/MRE11_METJA MRE11_METJA] Involved in DNA double-strand break repair (DSBR). The Rad50/Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity (By similarity).		[https://www.uniprot.org/uniprot/MRE11_METJA MRE11_METJA] Involved in DNA double-strand break repair (DSBR). The Rad50/Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity (By similarity).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	ATP-dependent DNA end recognition and nucleolytic processing are central functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair. However, it is still unclear how ATP binding and hydrolysis primes the MR function and regulates repair pathway choice in cells. Here, Methanococcus jannaschii MR-ATPgammaS-DNA structure reveals that the partly deformed DNA runs symmetrically across central groove between two ATPgammaS-bound Rad50 nucleotide-binding domains. Duplex DNA cannot access the Mre11 active site in the ATP-free full-length MR complex. ATP hydrolysis drives rotation of the nucleotide-binding domain and induces the DNA melting so that the substrate DNA can access Mre11. Our findings suggest that the ATP hydrolysis-driven conformational changes in both DNA and the MR complex coordinate the melting and endonuclease activity.
-
-	ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex.,Liu Y, Sung S, Kim Y, Li F, Gwon G, Jo A, Kim AK, Kim T, Song OK, Lee SE, Cho Y EMBO J. 2015 Dec 30. pii: e201592462. PMID:26717941<ref>PMID:26717941</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5f3w" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[ATPase 3D structures\|ATPase 3D structures]]		*[[ATPase 3D structures\|ATPase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:45, 12 July 2023

OCA — Wed, 12 Jul 2023 08:45:13 GMT

←Older revision		Revision as of 08:45, 12 July 2023
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	<StructureSection load='5f3w' size='340' side='right'caption='[[5f3w]], [[Resolution\|resolution]] 3.11Å' scene=''>		<StructureSection load='5f3w' size='340' side='right'caption='[[5f3w]], [[Resolution\|resolution]] 3.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f3w]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Metja Metja~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F3W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5F3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f3w]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F3W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID~~-~~ADENYLATE+ESTER'>AGS</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.11Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~mre11, MJ1323 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=243232 METJA]), rad50, MJ1322 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=243232 METJA])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5f3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f3w OCA], [~~http~~://pdbe.org/5f3w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5f3w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5f3w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5f3w ProSAT]</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=5f3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f3w OCA], [https://pdbe.org/5f3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f3w RCSB], [https://www.ebi.ac.uk/pdbsum/5f3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f3w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MRE11_METJA MRE11_METJA]] Involved in DNA double-strand break repair (DSBR). The Rad50/Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity (By similarity). [[http://www.uniprot.org/uniprot/RAD50_METJA RAD50_METJA]] Involved in DNA double-strand break repair (DSBR). The Rad50/Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity. Rad50 provides an ATP-dependent control of Mre11 by unwinding and/or repositioning DNA ends into the Mre11 active site.[HAMAP-Rule:MF_00449]	+	[https://www.uniprot.org/uniprot/MRE11_METJA MRE11_METJA] Involved in DNA double-strand break repair (DSBR). The Rad50/Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Metja~~]]	+	[[Category: Methanocaldococcus jannaschii DSM 2661]]
-	[[Category: ~~Liu, Y~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Complex]]~~	+	[[Category: Liu Y]]
-	~~[[Category: Dna binding protein-hydrolase-dna complex]]~~	+
-	~~[[Category: Nuclease~~]]	+

OCA at 07:58, 29 April 2020

OCA — Wed, 29 Apr 2020 07:58:39 GMT

←Older revision		Revision as of 07:58, 29 April 2020
Line 1:		Line 1:

	==Structure of the ATPrS-Mre11/Rad50-DNA complex==		==Structure of the ATPrS-Mre11/Rad50-DNA complex==
-	<StructureSection load='5f3w' size='340' side='right' caption='[[5f3w]], [[Resolution\|resolution]] 3.11Å' scene=''>	+	<StructureSection load='5f3w' size='340' side='right'caption='[[5f3w]], [[Resolution\|resolution]] 3.11Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f3w]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F3W OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5F3W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f3w]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F3W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5F3W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5f3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f3w OCA], [http://pdbe.org/5f3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f3w RCSB], [http://www.ebi.ac.uk/pdbsum/5f3w PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mre11, MJ1323 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA]), rad50, MJ1322 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</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=5f3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f3w OCA], [http://pdbe.org/5f3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f3w RCSB], [http://www.ebi.ac.uk/pdbsum/5f3w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f3w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5f3w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5f3w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[ATPase 3D structures\|ATPase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Metja]]
	[[Category: Liu, Y]]		[[Category: Liu, Y]]
	[[Category: Complex]]		[[Category: Complex]]
	[[Category: Dna binding protein-hydrolase-dna complex]]		[[Category: Dna binding protein-hydrolase-dna complex]]
	[[Category: Nuclease]]		[[Category: Nuclease]]

OCA at 15:12, 2 March 2016

OCA — Wed, 02 Mar 2016 15:12:15 GMT

←Older revision		Revision as of 15:12, 2 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5f3w is ~~ON HOLD until Paper~~ Publication	+	==Structure of the ATPrS-Mre11/Rad50-DNA complex==
		+	<StructureSection load='5f3w' size='340' side='right' caption='[[5f3w]], [[Resolution\|resolution]] 3.11Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5f3w]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F3W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F3W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5f3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f3w OCA], [http://pdbe.org/5f3w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f3w RCSB], [http://www.ebi.ac.uk/pdbsum/5f3w PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MRE11_METJA MRE11_METJA]] Involved in DNA double-strand break repair (DSBR). The Rad50/Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity (By similarity). [[http://www.uniprot.org/uniprot/RAD50_METJA RAD50_METJA]] Involved in DNA double-strand break repair (DSBR). The Rad50/Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity. Rad50 provides an ATP-dependent control of Mre11 by unwinding and/or repositioning DNA ends into the Mre11 active site.[HAMAP-Rule:MF_00449]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	ATP-dependent DNA end recognition and nucleolytic processing are central functions of the Mre11/Rad50 (MR) complex in DNA double-strand break repair. However, it is still unclear how ATP binding and hydrolysis primes the MR function and regulates repair pathway choice in cells. Here, Methanococcus jannaschii MR-ATPgammaS-DNA structure reveals that the partly deformed DNA runs symmetrically across central groove between two ATPgammaS-bound Rad50 nucleotide-binding domains. Duplex DNA cannot access the Mre11 active site in the ATP-free full-length MR complex. ATP hydrolysis drives rotation of the nucleotide-binding domain and induces the DNA melting so that the substrate DNA can access Mre11. Our findings suggest that the ATP hydrolysis-driven conformational changes in both DNA and the MR complex coordinate the melting and endonuclease activity.

-	~~Authors: Yaqi~~, L.	+	ATP-dependent DNA binding, unwinding, and resection by the Mre11/Rad50 complex.,Liu Y, Sung S, Kim Y, Li F, Gwon G, Jo A, Kim AK, Kim T, Song OK, Lee SE, Cho Y EMBO J. 2015 Dec 30. pii: e201592462. PMID:26717941<ref>PMID:26717941</ref>

-	~~Description~~: ~~Nuclease~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Yaqi, L~~]]	+	<div class="pdbe-citations 5f3w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Liu, Y]]
		+	[[Category: Complex]]
		+	[[Category: Dna binding protein-hydrolase-dna complex]]
		+	[[Category: Nuclease]]

OCA at 12:31, 16 December 2015

OCA — Wed, 16 Dec 2015 12:31:26 GMT

←Older revision		Revision as of 12:31, 16 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5f3w is ON HOLD	+	The entry 5f3w is ON HOLD until Paper Publication

	Authors: Yaqi, L.		Authors: Yaqi, L.

-	Description: ~~Unknown protein~~	+	Description: Nuclease
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yaqi, L]]		[[Category: Yaqi, L]]

OCA: Protected "5f3w" [edit=sysop:move=sysop]

OCA — Wed, 09 Dec 2015 12:35:19 GMT

Protected "5f3w" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:35, 9 December 2015

OCA: New page: '''Unreleased structure''' The entry 5f3w is ON HOLD Authors: Yaqi, L. Description: Unknown protein Category: Unreleased Structures Category: Yaqi, L

OCA — Wed, 09 Dec 2015 12:35:18 GMT

New page: '''Unreleased structure''' The entry 5f3w is ON HOLD Authors: Yaqi, L. Description: Unknown protein Category: Unreleased Structures Category: Yaqi, L

New page

'''Unreleased structure'''

The entry 5f3w is ON HOLD

Authors: Yaqi, L.

Description: Unknown protein
[[Category: Unreleased Structures]]
[[Category: Yaqi, L]]