6i58 - Revision history

OCA at 11:47, 24 January 2024

OCA — Wed, 24 Jan 2024 11:47:09 GMT

←Older revision		Revision as of 11:47, 24 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6i58]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2f83 2f83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I58 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6i58]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2f83 2f83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I58 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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.6Å</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6i58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i58 OCA], [https://pdbe.org/6i58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i58 RCSB], [https://www.ebi.ac.uk/pdbsum/6i58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i58 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=6i58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i58 OCA], [https://pdbe.org/6i58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i58 RCSB], [https://www.ebi.ac.uk/pdbsum/6i58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i58 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:26, 8 March 2023

OCA — Wed, 08 Mar 2023 07:26:12 GMT

←Older revision		Revision as of 07:26, 8 March 2023
Line 3:		Line 3:
	<StructureSection load='6i58' size='340' side='right'caption='[[6i58]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6i58' size='340' side='right'caption='[[6i58]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i58]] is a 1 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=6I58 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I58 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i58]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2f83 2f83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I58 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene~~></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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6i44\|6i44]], [[6i4w\|6i4w]]</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=6i58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i58 OCA], [https://pdbe.org/6i58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i58 RCSB], [https://www.ebi.ac.uk/pdbsum/6i58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i58 ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_XIa Coagulation factor XIa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.27 3.4.21.27] </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=6i58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i58 OCA], [~~http~~://pdbe.org/6i58 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i58 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i58 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i58 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN]] Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:[~~http~~://omim.org/entry/612416 612416]]; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.<ref>PMID:2813350</ref> <ref>PMID:1547342</ref> <ref>PMID:7888672</ref> <ref>PMID:7669672</ref> <ref>PMID:9401068</ref> <ref>PMID:9787168</ref> <ref>PMID:10027710</ref> <ref>PMID:10606881</ref> <ref>PMID:11895778</ref> <ref>PMID:15026311</ref> <ref>PMID:15180874</ref> <ref>PMID:15953011</ref> <ref>PMID:16607084</ref> <ref>PMID:18005151</ref> <ref>PMID:21668437</ref> <ref>PMID:21457405</ref> <ref>PMID:22016685</ref> <ref>PMID:22322133</ref> <ref>PMID:21999818</ref> <ref>PMID:22159456</ref>	+	[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:[https://omim.org/entry/612416 612416]; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.<ref>PMID:2813350</ref> <ref>PMID:1547342</ref> <ref>PMID:7888672</ref> <ref>PMID:7669672</ref> <ref>PMID:9401068</ref> <ref>PMID:9787168</ref> <ref>PMID:10027710</ref> <ref>PMID:10606881</ref> <ref>PMID:11895778</ref> <ref>PMID:15026311</ref> <ref>PMID:15180874</ref> <ref>PMID:15953011</ref> <ref>PMID:16607084</ref> <ref>PMID:18005151</ref> <ref>PMID:21668437</ref> <ref>PMID:21457405</ref> <ref>PMID:22016685</ref> <ref>PMID:22322133</ref> <ref>PMID:21999818</ref> <ref>PMID:22159456</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN]] Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.	+	[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6i58" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6i58" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Factor XIa 3D structures\|Factor XIa 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Coagulation factor XIa]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dreveny, I]]	+	[[Category: Dreveny I]]
-	[[Category: Emsley, J]]	+	[[Category: Emsley J]]
-	[[Category: Li, C]]	+	[[Category: Li C]]
-	[[Category: McCrae, K]]	+	[[Category: McCrae K]]
-	[[Category: Pathak, M]]	+	[[Category: Pathak M]]
-	~~[[Category: Activation]]~~	+
-	~~[[Category: Blood clotting]]~~	+
-	~~[[Category: Factor xi]]~~	+
-	~~[[Category: High molecular weight kininogen]]~~	+
-	~~[[Category: Prekallikrein~~]]	+

OCA at 13:37, 10 May 2019

OCA — Fri, 10 May 2019 13:37:13 GMT

←Older revision		Revision as of 13:37, 10 May 2019
Line 1:		Line 1:

	==Allosteric activation of human prekallikrein by apple domain disc rotation==		==Allosteric activation of human prekallikrein by apple domain disc rotation==
-	<StructureSection load='6i58' size='340' side='right' caption='[[6i58]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='6i58' size='340' side='right'caption='[[6i58]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6i58]] is a 1 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=6I58 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I58 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6i58]] is a 1 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=6I58 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I58 FirstGlance]. <br>
Line 28:		Line 28:
	[[Category: Coagulation factor XIa]]		[[Category: Coagulation factor XIa]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
	[[Category: Dreveny, I]]		[[Category: Dreveny, I]]
	[[Category: Emsley, J]]		[[Category: Emsley, J]]

OCA at 07:29, 6 March 2019

OCA — Wed, 06 Mar 2019 07:29:57 GMT

←Older revision		Revision as of 07:29, 6 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6i58 is ~~ON HOLD~~	+	==Allosteric activation of human prekallikrein by apple domain disc rotation==
		+	<StructureSection load='6i58' size='340' side='right' caption='[[6i58]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6i58]] is a 1 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=6I58 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I58 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6i44\|6i44]], [[6i4w\|6i4w]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coagulation_factor_XIa Coagulation factor XIa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.27 3.4.21.27] </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=6i58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i58 OCA], [http://pdbe.org/6i58 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i58 RCSB], [http://www.ebi.ac.uk/pdbsum/6i58 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i58 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN]] Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:[http://omim.org/entry/612416 612416]]; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.<ref>PMID:2813350</ref> <ref>PMID:1547342</ref> <ref>PMID:7888672</ref> <ref>PMID:7669672</ref> <ref>PMID:9401068</ref> <ref>PMID:9787168</ref> <ref>PMID:10027710</ref> <ref>PMID:10606881</ref> <ref>PMID:11895778</ref> <ref>PMID:15026311</ref> <ref>PMID:15180874</ref> <ref>PMID:15953011</ref> <ref>PMID:16607084</ref> <ref>PMID:18005151</ref> <ref>PMID:21668437</ref> <ref>PMID:21457405</ref> <ref>PMID:22016685</ref> <ref>PMID:22322133</ref> <ref>PMID:21999818</ref> <ref>PMID:22159456</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN]] Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Plasma prekallikrein (PK) and Factor XI (FXI) are apple domain containing serine proteases which when activated to PKa and FXIa cleave substrates kininogen, Factor XII and Factor IX respectively directing plasma coagulation, bradykinin release, inflammation and thrombosis pathways. OBJECTIVE: To investigate the three-dimensional structure of full-length PKa and perform a comparison with FXI. METHODS: A series of recombinant full-length PKa and FXI constructs and variants were developed and the crystal structures determined. RESULTS AND CONCLUSIONS: A 1.3 A structure of full-length PKa reveals the protease domain positioned above a disc-shaped assemblage of four apple domains in an active conformation. A comparison with the homologous FXI structure reveals the intramolecular disulphide and structural differences in the apple 4 domain that prevents dimer formation in PKa as opposed to FXI. Two latch-like loops (LL1 and LL2) extend from the PKa protease domain to form interactions with the apple 1 and apple 3 domains respectively. A major unexpected difference in the PKa structure compared to FXI is the 180 masculine disc rotation of the apple domains relative to the protease domain. This results in a switched configuration of the latch loops such that LL2 interacts and buries portions of the apple 3 domain in the FXI zymogen whereas in PKa LL2 interacts with the apple 1 domain. Hydrogen-deuterium exchange mass spectrometry on plasma purified human PK and PKa determined that regions of the apple 3 domain have increased surface exposure in PKa compared to the zymogen PK suggesting conformational change upon activation. This article is protected by copyright. All rights reserved.

-	~~Authors: Li~~, C., ~~Pathak~~, M., McCrae~~, K.~~, Dreveny, I., ~~Emsley~~, J.	+	Plasma Kallikrein Structure Reveals Apple Domain Disc Rotated Conformation Compared to Factor XI.,Li C, Voos KM, Pathak M, Hall G, McCrae KR, Dreveny I, Li R, Emsley J J Thromb Haemost. 2019 Feb 23. doi: 10.1111/jth.14418. PMID:30801944<ref>PMID:30801944</ref>

-	~~Description: Allosteric activation~~ of ~~human prekallikrein by apple domain disc rotation~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Li, C]]~~	+	<div class="pdbe-citations 6i58" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Emsley, J~~]]	+	== References ==
-	[[Category: ~~Mccrae, K~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Coagulation factor XIa]]
		+	[[Category: Homo sapiens]]
	[[Category: Dreveny, I]]		[[Category: Dreveny, I]]
		+	[[Category: Emsley, J]]
		+	[[Category: Li, C]]
		+	[[Category: McCrae, K]]
	[[Category: Pathak, M]]		[[Category: Pathak, M]]
		+	[[Category: Activation]]
		+	[[Category: Blood clotting]]
		+	[[Category: Factor xi]]
		+	[[Category: High molecular weight kininogen]]
		+	[[Category: Prekallikrein]]

OCA: Protected "6i58" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 18:34:48 GMT

Protected "6i58" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:34, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6i58 is ON HOLD Authors: Li, C., Pathak, M., McCrae, K., Dreveny, I., Emsley, J. Description: Allosteric activation of human prekallikrein by apple...

OCA — Sun, 02 Dec 2018 18:34:47 GMT

New page: '''Unreleased structure''' The entry 6i58 is ON HOLD Authors: Li, C., Pathak, M., McCrae, K., Dreveny, I., Emsley, J. Description: Allosteric activation of human prekallikrein by apple...

New page

'''Unreleased structure'''

The entry 6i58 is ON HOLD

Authors: Li, C., Pathak, M., McCrae, K., Dreveny, I., Emsley, J.

Description: Allosteric activation of human prekallikrein by apple domain disc rotation
[[Category: Unreleased Structures]]
[[Category: Li, C]]
[[Category: Emsley, J]]
[[Category: Mccrae, K]]
[[Category: Dreveny, I]]
[[Category: Pathak, M]]