6jkn - Revision history

OCA at 10:38, 27 March 2024

2024-03-27T10:38:29Z

←Older revision		Revision as of 10:38, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6jkn' size='340' side='right'caption='[[6jkn]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6jkn' size='340' side='right'caption='[[6jkn]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jkn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JKN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JKN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jkn]] is a 1 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=6JKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JKN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=K:POTASSIUM+ION'>K</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]] 1.401Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=6jkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jkn OCA], [~~http~~://pdbe.org/6jkn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jkn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jkn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jkn 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=6jkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jkn OCA], [https://pdbe.org/6jkn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jkn RCSB], [https://www.ebi.ac.uk/pdbsum/6jkn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jkn ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Human telomeric guanine-rich DNA, which could adopt different G-quadruplex structures, plays important roles in protecting the cell from recombination and degradation. Although many of these structures were determined, the chair-type G-quadruplex structure remains elusive. Here, we present a crystal structure of the G-quadruplex composed of the human telomeric sequence d[GGGTTAGG8GTTAGGGTTAGG20G] with two dG to 8Br-dG substitutions at positions 8 and 20 with syn conformation in the K+ solution. It forms a novel three-layer chair-type G-quadruplex with two linking trinucleotide loops. Particularly, T5 and T17 are coplanar with two water molecules stacking on the G-tetrad layer in a sandwich-like mode through a coordinating K+ ion and an A6A18 base pair. While a twisted Hoogsteen A12T10 base pair caps on the top of G-tetrad core. The three linking TTA loops are edgewise and each DNA strand has two antiparallel adjacent strands. Our findings contribute to a deeper understanding and highlight the unique roles of loop and water molecule in the folding of the G-quadruplex.
-
-	The crystal structure of an antiparallel chair-type G-quadruplex formed by Bromo-substituted human telomeric DNA.,Geng Y, Liu C, Zhou B, Cai Q, Miao H, Shi X, Xu N, You Y, Fung CP, Din RU, Zhu G Nucleic Acids Res. 2019 Apr 8. pii: 5430838. doi: 10.1093/nar/gkz221. PMID:30957851<ref>PMID:30957851</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6jkn" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cai, Q]]	+	[[Category: Cai Q]]
-	[[Category: Geng, Y]]	+	[[Category: Geng Y]]
-	[[Category: Liu, C]]	+	[[Category: Liu C]]
-	[[Category: Zhu, G]]	+	[[Category: Zhu G]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: G-quadruplex~~]]	+

OCA at 08:15, 24 April 2019

2019-04-24T08:15:27Z

←Older revision		Revision as of 08:15, 24 April 2019
Line 8:		Line 8:
	<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=6jkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jkn OCA], [http://pdbe.org/6jkn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jkn RCSB], [http://www.ebi.ac.uk/pdbsum/6jkn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jkn 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=6jkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jkn OCA], [http://pdbe.org/6jkn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jkn RCSB], [http://www.ebi.ac.uk/pdbsum/6jkn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jkn ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human telomeric guanine-rich DNA, which could adopt different G-quadruplex structures, plays important roles in protecting the cell from recombination and degradation. Although many of these structures were determined, the chair-type G-quadruplex structure remains elusive. Here, we present a crystal structure of the G-quadruplex composed of the human telomeric sequence d[GGGTTAGG8GTTAGGGTTAGG20G] with two dG to 8Br-dG substitutions at positions 8 and 20 with syn conformation in the K+ solution. It forms a novel three-layer chair-type G-quadruplex with two linking trinucleotide loops. Particularly, T5 and T17 are coplanar with two water molecules stacking on the G-tetrad layer in a sandwich-like mode through a coordinating K+ ion and an A6A18 base pair. While a twisted Hoogsteen A12T10 base pair caps on the top of G-tetrad core. The three linking TTA loops are edgewise and each DNA strand has two antiparallel adjacent strands. Our findings contribute to a deeper understanding and highlight the unique roles of loop and water molecule in the folding of the G-quadruplex.
		+
		+	The crystal structure of an antiparallel chair-type G-quadruplex formed by Bromo-substituted human telomeric DNA.,Geng Y, Liu C, Zhou B, Cai Q, Miao H, Shi X, Xu N, You Y, Fung CP, Din RU, Zhu G Nucleic Acids Res. 2019 Apr 8. pii: 5430838. doi: 10.1093/nar/gkz221. PMID:30957851<ref>PMID:30957851</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jkn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:04, 3 April 2019

2019-04-03T07:04:56Z

←Older revision		Revision as of 07:04, 3 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6jkn is ON HOLD until Paper Publication~~	+	==Crystal Structure of G-quadruplex Formed by Bromo-substituted Human Telomeric DNA==
-		+	<StructureSection load='6jkn' size='340' side='right'caption='[[6jkn]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors: Geng, Y., Cai, Q., Liu, C., Zhu, G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jkn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JKN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JKN FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of G-quadruplex Formed by Bromo-substituted Human Telomeric DNA	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene></td></tr>
-	[[~~Category~~: ~~Zhu~~, G]]	+	<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=6jkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jkn OCA], [http://pdbe.org/6jkn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jkn RCSB], [http://www.ebi.ac.uk/pdbsum/6jkn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jkn ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Cai, Q]]		[[Category: Cai, Q]]
		+	[[Category: Geng, Y]]
	[[Category: Liu, C]]		[[Category: Liu, C]]
-	[[Category: ~~Geng~~, Y]]	+	[[Category: Zhu, G]]
		+	[[Category: Dna]]
		+	[[Category: G-quadruplex]]

OCA at 04:51, 27 March 2019

2019-03-27T04:51:10Z

←Older revision		Revision as of 04:51, 27 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Geng, Y., Cai, Q., Liu, C., Zhu, G.		Authors: Geng, Y., Cai, Q., Liu, C., Zhu, G.

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

2019-03-06T05:35:10Z

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

←Older revision

Revision as of 05:35, 6 March 2019

OCA: New page: '''Unreleased structure''' The entry 6jkn is ON HOLD Authors: Geng, Y., Cai, Q., Liu, C., Zhu, G. Description: Crystal Structure of G-quadruplex Formed by Bromo-substituted Human Telom...

2019-03-06T05:35:08Z

New page: '''Unreleased structure''' The entry 6jkn is ON HOLD Authors: Geng, Y., Cai, Q., Liu, C., Zhu, G. Description: Crystal Structure of G-quadruplex Formed by Bromo-substituted Human Telom...

New page

'''Unreleased structure'''

The entry 6jkn is ON HOLD

Authors: Geng, Y., Cai, Q., Liu, C., Zhu, G.

Description: Crystal Structure of G-quadruplex Formed by Bromo-substituted Human Telomeric DNA
[[Category: Unreleased Structures]]
[[Category: Zhu, G]]
[[Category: Cai, Q]]
[[Category: Liu, C]]
[[Category: Geng, Y]]