7m0b - Revision history

OCA at 09:21, 25 October 2023

OCA — Wed, 25 Oct 2023 09:21:25 GMT

←Older revision		Revision as of 09:21, 25 October 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7m0b]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=7M0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7M0B FirstGlance]. <br>		<table><tr><td colspan='2'>[[7m0b]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=7M0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7M0B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=7m0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7m0b OCA], [https://pdbe.org/7m0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7m0b RCSB], [https://www.ebi.ac.uk/pdbsum/7m0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7m0b 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=7m0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7m0b OCA], [https://pdbe.org/7m0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7m0b RCSB], [https://www.ebi.ac.uk/pdbsum/7m0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7m0b ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:33, 15 February 2023

OCA — Wed, 15 Feb 2023 10:33:10 GMT

←Older revision		Revision as of 10:33, 15 February 2023
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-	====	+	==Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound mismatched DSB and incoming dUMPNPP==
-	<StructureSection load='7m0b' size='340' side='right'caption='[[7m0b]]' scene=''>	+	<StructureSection load='7m0b' size='340' side='right'caption='[[7m0b]], [[Resolution\|resolution]] 2.00Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7m0b]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=7M0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7M0B 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=7m0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7m0b OCA], [https://pdbe.org/7m0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7m0b RCSB], [https://www.ebi.ac.uk/pdbsum/7m0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7m0b 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=7m0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7m0b OCA], [https://pdbe.org/7m0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7m0b RCSB], [https://www.ebi.ac.uk/pdbsum/7m0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7m0b ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPOLL_HUMAN DPOLL_HUMAN] Repair polymerase. Involved in base excision repair (BER) responsible for repair of lesions that give rise to abasic (AP) sites in DNA. Has both DNA polymerase and terminal transferase activities. Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.<ref>PMID:11457865</ref> <ref>PMID:15537631</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA double-strand breaks (DSBs) threaten genomic stability, since their persistence can lead to loss of critical genetic information, chromosomal translocations or rearrangements, and cell death. DSBs can be repaired through the nonhomologous end-joining pathway (NHEJ), which processes and ligates DNA ends efficiently to prevent or minimize sequence loss. Polymerase lambda (Pollambda), one of the Family X polymerases, fills sequence gaps of DSB substrates with a strict specificity for a base-paired primer terminus. There is little information regarding Pollambda's approach to engaging such substrates. We used in vitro polymerization and cell-based NHEJ assays to explore the contributions of conserved loop regions toward DSB substrate specificity and utilization. In addition, we present multiple crystal structures of Pollambda in synapsis with varying biologically relevant DSB end configurations, revealing how key structural features and hydrogen bonding networks work in concert to stabilize these tenuous, potentially cytotoxic DNA lesions during NHEJ.
		+
		+	Analysis of diverse double-strand break synapsis with Pollambda reveals basis for unique substrate specificity in nonhomologous end-joining.,Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC Nat Commun. 2022 Jul 1;13(1):3806. doi: 10.1038/s41467-022-31278-4. PMID:35778389<ref>PMID:35778389</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7m0b" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Bebenek K]]
		+	[[Category: Kaminski AM]]
		+	[[Category: Kunkel TA]]
		+	[[Category: Pedersen LC]]

OCA at 06:13, 16 March 2022

OCA — Wed, 16 Mar 2022 06:13:37 GMT

←Older revision		Revision as of 06:13, 16 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7m0b ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7m0b' size='340' side='right'caption='[[7m0b]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7m0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7m0b OCA], [https://pdbe.org/7m0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7m0b RCSB], [https://www.ebi.ac.uk/pdbsum/7m0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7m0b ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:31, 24 March 2021

OCA — Wed, 24 Mar 2021 05:31:29 GMT

←Older revision		Revision as of 05:31, 24 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7m0b is ON HOLD	+	The entry 7m0b is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7m0b" [edit=sysop:move=sysop]

OCA — Wed, 17 Mar 2021 05:27:52 GMT

Protected "7m0b" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:27, 17 March 2021

OCA: New page: '''Unreleased structure''' The entry 7m0b is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 17 Mar 2021 05:27:51 GMT

New page: '''Unreleased structure''' The entry 7m0b is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7m0b is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]