5ew1 - Revision history

OCA at 08:28, 12 July 2023

OCA — Wed, 12 Jul 2023 08:28:09 GMT

←Older revision		Revision as of 08:28, 12 July 2023
Line 3:		Line 3:
	<StructureSection load='5ew1' size='340' side='right'caption='[[5ew1]], [[Resolution\|resolution]] 2.95Å' scene=''>		<StructureSection load='5ew1' size='340' side='right'caption='[[5ew1]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ew1]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EW1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5EW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ew1]] 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=5EW1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EW1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0G6:D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE'>0G6</scene>, <scene name='pdbligand=NA:~~SODIUM+ION~~'>NA</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL-D-GLUCOSAMINE~~'>~~NAG~~</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]] 2.95Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~3DR~~:~~1,2~~-~~DIDEOXYRIBOFURANOSE~~-5-~~PHOSPHATE~~'>~~3DR~~</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0G6:D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE'>0G6</scene>, <scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </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=5ew1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ew1 OCA], [https://pdbe.org/5ew1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ew1 RCSB], [https://www.ebi.ac.uk/pdbsum/5ew1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ew1 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=5ew1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ew1 OCA], [~~http~~://pdbe.org/5ew1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ew1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ew1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ew1 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[~~http~~://omim.org/entry/613679 613679]]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[~~http~~://omim.org/entry/601367 601367]]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[~~http~~://omim.org/entry/188050 188050]]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[~~http~~://omim.org/entry/614390 614390]]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>	+	[https://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[https://omim.org/entry/613679 613679]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[https://omim.org/entry/601367 601367]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[https://omim.org/entry/188050 188050]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[https://omim.org/entry/614390 614390]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.<ref>PMID:2856554</ref>	+	[https://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.<ref>PMID:2856554</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 31:		Line 30:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Thrombin]]~~	+	[[Category: Parente V]]
-	~~[[Category: Krauss, I Russo]]~~	+	[[Category: Pica A]]
-	[[Category: Parente, V]]	+	[[Category: Russo Krauss I]]
-	[[Category: Pica, A]]	+	[[Category: Sica F]]
-	[[Category: ~~Sica, F~~]]	+
-	[[Category: ~~Abasic furan]]~~	+
-	~~[[Category: Blood coagulation]]~~	+
-	~~[[Category: Dna aptamer]]~~	+
-	~~[[Category: Dna-inhibitor]]~~	+
-	~~[[Category: Duplex-quadruplex junction]]~~	+
-	~~[[Category: G-quadruplex]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Serine protease~~]]	+

OCA at 07:46, 29 April 2020

OCA — Wed, 29 Apr 2020 07:46:55 GMT

←Older revision		Revision as of 07:46, 29 April 2020
Line 1:		Line 1:

	==Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3==		==Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3==
-	<StructureSection load='5ew1' size='340' side='right' caption='[[5ew1]], [[Resolution\|resolution]] 2.95Å' scene=''>	+	<StructureSection load='5ew1' size='340' side='right'caption='[[5ew1]], [[Resolution\|resolution]] 2.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ew1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EW1 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EW1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ew1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EW1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EW1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0G6:D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE'>0G6</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0G6:D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE'>0G6</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </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=5ew1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ew1 OCA], [http://pdbe.org/5ew1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ew1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ew1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ew1 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=5ew1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ew1 OCA], [http://pdbe.org/5ew1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ew1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ew1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ew1 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 22:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 5ew1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ew1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thrombin 3D Structures\|Thrombin 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
	[[Category: Thrombin]]		[[Category: Thrombin]]
	[[Category: Krauss, I Russo]]		[[Category: Krauss, I Russo]]

OCA at 11:45, 15 December 2016

OCA — Thu, 15 Dec 2016 11:45:00 GMT

←Older revision		Revision as of 11:45, 15 December 2016
Line 15:		Line 15:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Potent second-generation~~ thrombin aptamers ~~adopt a duplex-quadruplex bimodular folding~~ and ~~recognize thrombin~~ exosite II ~~with~~ very ~~high~~ affinity ~~and specificity~~. ~~A sound model of these oligonucleotides~~, ~~either free or~~ in ~~complex~~ with thrombin~~, is not yet available~~. ~~Here~~, ~~a structural study~~ of ~~one of these aptamers, HD22-27mer~~, is presented. The ~~crystal structure of this aptamer in complex with thrombin displays a novel architecture in which~~ the ~~helical stem is enchained to a pseudo-G-quadruplex~~. The ~~results also underline~~ the ~~role~~ of the ~~residues that join the duplex~~ and ~~quadruplex motifs and control their recruitment in thrombin binding~~.	+	Aptamers directed against human thrombin can selectively bind to two different exosites on the protein surface. The simultaneous use of two DNA aptamers, HD1 and HD22, directed to exosite I and exosite II respectively, is a very powerful approach to exploit their combined affinity. Indeed, strategies to link HD1 and HD22 together have been proposed in order to create a single bivalent molecule with an enhanced ability to control thrombin activity. In this work, the crystal structures of two ternary complexes, in which thrombin is sandwiched between two DNA aptamers, are presented and discussed. The structures shed light on the cross talk between the two exosites. The through-bond effects are particularly evident at exosite II, with net consequences on the HD22 structure. Moreover, thermodynamic data on the binding of the two aptamers are also reported and analyzed.

-	~~Duplex~~-~~quadruplex motifs~~ in ~~a peculiar structural organization cooperatively contribute to thrombin binding~~ of a DNA ~~aptamer~~.,Russo Krauss I, ~~Pica A~~, ~~Merlino A~~, ~~Mazzarella L~~, Sica F ~~Acta Crystallogr D Biol Crystallogr~~. ~~2013 Dec;69(Pt 12):2403-11~~. ~~doi~~:~~, 10.1107/S0907444913022269. Epub 2013 Nov 19~~. PMID:~~24311581~~<ref>PMID:~~24311581~~</ref>	+	Through-bond effects in the ternary complexes of thrombin sandwiched by two DNA aptamers.,Pica A, Russo Krauss I, Parente V, Tateishi-Karimata H, Nagatoishi S, Tsumoto K, Sugimoto N, Sica F Nucleic Acids Res. 2016 Nov 28. pii: gkw1113. PMID:27899589<ref>PMID:27899589</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 18:30, 10 December 2016

OCA — Sat, 10 Dec 2016 18:30:48 GMT

←Older revision		Revision as of 18:30, 10 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~5ew1~~ is ~~ON HOLD~~ until ~~Paper~~ Publication	+	==Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3==
		+	<StructureSection load='5ew1' size='340' side='right' caption='[[5ew1]], [[Resolution\|resolution]] 2.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ew1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EW1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EW1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0G6:D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE'>0G6</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] </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=5ew1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ew1 OCA], [http://pdbe.org/5ew1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ew1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ew1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ew1 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[http://omim.org/entry/613679 613679]]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[http://omim.org/entry/601367 601367]]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[http://omim.org/entry/188050 188050]]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[http://omim.org/entry/614390 614390]]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN]] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.<ref>PMID:2856554</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Potent second-generation thrombin aptamers adopt a duplex-quadruplex bimodular folding and recognize thrombin exosite II with very high affinity and specificity. A sound model of these oligonucleotides, either free or in complex with thrombin, is not yet available. Here, a structural study of one of these aptamers, HD22-27mer, is presented. The crystal structure of this aptamer in complex with thrombin displays a novel architecture in which the helical stem is enchained to a pseudo-G-quadruplex. The results also underline the role of the residues that join the duplex and quadruplex motifs and control their recruitment in thrombin binding.

-	~~Authors: Pica, A~~., Russo Krauss, I., ~~Parente~~, V., ~~Sica~~, F.	+	Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer.,Russo Krauss I, Pica A, Merlino A, Mazzarella L, Sica F Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2403-11. doi:, 10.1107/S0907444913022269. Epub 2013 Nov 19. PMID:24311581<ref>PMID:24311581</ref>

-	~~Description~~: ~~Human thrombin sandwiched between two DNA aptamers~~: ~~HD22 and HD1-deltaT3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ew1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Thrombin]]
		+	[[Category: Krauss, I Russo]]
	[[Category: Parente, V]]		[[Category: Parente, V]]
-	[[Category: Russo Krauss, I]]
-	[[Category: Sica, F]]
	[[Category: Pica, A]]		[[Category: Pica, A]]
		+	[[Category: Sica, F]]
		+	[[Category: Abasic furan]]
		+	[[Category: Blood coagulation]]
		+	[[Category: Dna aptamer]]
		+	[[Category: Dna-inhibitor]]
		+	[[Category: Duplex-quadruplex junction]]
		+	[[Category: G-quadruplex]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Protein-dna complex]]
		+	[[Category: Serine protease]]

OCA at 10:52, 19 October 2016

OCA — Wed, 19 Oct 2016 10:52:38 GMT

←Older revision		Revision as of 10:52, 19 October 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ew1 is ON HOLD	+	The entry 5ew1 is ON HOLD until Paper Publication

	Authors: Pica, A., Russo Krauss, I., Parente, V., Sica, F.		Authors: Pica, A., Russo Krauss, I., Parente, V., Sica, F.

OCA: Protected "5ew1" [edit=sysop:move=sysop]

OCA — Tue, 01 Dec 2015 03:27:43 GMT

Protected "5ew1" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:27, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5ew1 is ON HOLD Authors: Pica, A., Russo Krauss, I., Parente, V., Sica, F. Description: Human thrombin sandwiched between two DNA aptamers: HD22 an...

OCA — Tue, 01 Dec 2015 03:27:41 GMT

New page: '''Unreleased structure''' The entry 5ew1 is ON HOLD Authors: Pica, A., Russo Krauss, I., Parente, V., Sica, F. Description: Human thrombin sandwiched between two DNA aptamers: HD22 an...

New page

'''Unreleased structure'''

The entry 5ew1 is ON HOLD

Authors: Pica, A., Russo Krauss, I., Parente, V., Sica, F.

Description: Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3
[[Category: Unreleased Structures]]
[[Category: Parente, V]]
[[Category: Russo Krauss, I]]
[[Category: Sica, F]]
[[Category: Pica, A]]