5vyg - Revision history

OCA at 14:02, 4 October 2023

OCA — Wed, 04 Oct 2023 14:02:43 GMT

←Older revision		Revision as of 14:02, 4 October 2023
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	==Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide==		==Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide==
-	<StructureSection load='5vyg' size='340' side='right' caption='[[5vyg]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5vyg' size='340' side='right'caption='[[5vyg]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vyg]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VYG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vyg]] is a 3 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=5VYG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VYG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</scene~~>, ~~<scene name='pdbligand=GXX:ALPHA-D-XYLOPYRANOSYL-(1- 3)-ALPHA-D-XYLOPYRANOSYL-(1- 3)-BETA-D-GLUCOPYRANOSE'>GXX</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]] 2.2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~F9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></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_IXa Coagulation factor IXa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.22 3.4.21.22]~~ </~~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=5vyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyg OCA], [https://pdbe.org/5vyg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vyg RCSB], [https://www.ebi.ac.uk/pdbsum/5vyg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyg 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=5vyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyg OCA], [~~http~~://pdbe.org/5vyg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vyg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vyg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyg ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN]] Defects in F9 are the cause of recessive X-linked hemophilia B (HEMB) [MIM:[~~http~~://omim.org/entry/306900 306900]]; also known as Christmas disease.<ref>PMID:8295821</ref> <ref>PMID:2592373</ref> <ref>PMID:2743975</ref> <ref>PMID:6603618</ref> <ref>PMID:3009023</ref> <ref>PMID:3790720</ref> <ref>PMID:3401602</ref> <ref>PMID:3243764</ref> <ref>PMID:2713493</ref> <ref>PMID:2714791</ref> <ref>PMID:2773937</ref> <ref>PMID:2775660</ref> <ref>PMID:2753873</ref> <ref>PMID:2738071</ref> <ref>PMID:2472424</ref> <ref>PMID:2339358</ref> <ref>PMID:2372509</ref> <ref>PMID:2162822</ref> <ref>PMID:1958666</ref> <ref>PMID:1902289</ref> <ref>PMID:1346975</ref> <ref>PMID:1615485</ref> <ref>PMID:8257988</ref> <ref>PMID:8076946</ref> <ref>PMID:8199596</ref> <ref>PMID:7981722</ref> <ref>PMID:8680410</ref> <ref>PMID:9222764</ref> <ref>PMID:9590153</ref> <ref>PMID:9452115</ref> <ref>PMID:9600455</ref> <ref>PMID:10698280</ref> <ref>PMID:10094553</ref> <ref>PMID:11122099</ref> <ref>PMID:12588353</ref> <ref>PMID:12604421</ref> Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide. Defects in F9 are the cause of thrombophilia due to factor IX defect (THPH8) [MIM:[~~http~~://omim.org/entry/300807 300807]]. A hemostatic disorder characterized by a tendency to thrombosis.<ref>PMID:19846852</ref>	+	[https://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN] Defects in F9 are the cause of recessive X-linked hemophilia B (HEMB) [MIM:[https://omim.org/entry/306900 306900]; also known as Christmas disease.<ref>PMID:8295821</ref> <ref>PMID:2592373</ref> <ref>PMID:2743975</ref> <ref>PMID:6603618</ref> <ref>PMID:3009023</ref> <ref>PMID:3790720</ref> <ref>PMID:3401602</ref> <ref>PMID:3243764</ref> <ref>PMID:2713493</ref> <ref>PMID:2714791</ref> <ref>PMID:2773937</ref> <ref>PMID:2775660</ref> <ref>PMID:2753873</ref> <ref>PMID:2738071</ref> <ref>PMID:2472424</ref> <ref>PMID:2339358</ref> <ref>PMID:2372509</ref> <ref>PMID:2162822</ref> <ref>PMID:1958666</ref> <ref>PMID:1902289</ref> <ref>PMID:1346975</ref> <ref>PMID:1615485</ref> <ref>PMID:8257988</ref> <ref>PMID:8076946</ref> <ref>PMID:8199596</ref> <ref>PMID:7981722</ref> <ref>PMID:8680410</ref> <ref>PMID:9222764</ref> <ref>PMID:9590153</ref> <ref>PMID:9452115</ref> <ref>PMID:9600455</ref> <ref>PMID:10698280</ref> <ref>PMID:10094553</ref> <ref>PMID:11122099</ref> <ref>PMID:12588353</ref> <ref>PMID:12604421</ref> Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide. Defects in F9 are the cause of thrombophilia due to factor IX defect (THPH8) [MIM:[https://omim.org/entry/300807 300807]. A hemostatic disorder characterized by a tendency to thrombosis.<ref>PMID:19846852</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN]] Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa.	+	[https://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN] Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5vyg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vyg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Factor IX 3D structures\|Factor IX 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Coagulation factor IXa~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Li~~, H L~~]]	+	[[Category: Li HL]]
-	[[Category: Yu~~, H J]]~~	+	[[Category: Yu HJ]]
-	~~[[Category: Egf repeat]]~~	+
-	~~[[Category: Glycosylation]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Notch regulation]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-hydrolase complex~~]]	+

OCA at 07:11, 28 February 2018

OCA — Wed, 28 Feb 2018 07:11:10 GMT

←Older revision		Revision as of 07:11, 28 February 2018
Line 3:		Line 3:
	<StructureSection load='5vyg' size='340' side='right' caption='[[5vyg]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5vyg' size='340' side='right' caption='[[5vyg]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vyg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vyg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GXX:ALPHA-D-XYLOPYRANOSYL-(1- 3)-ALPHA-D-XYLOPYRANOSYL-(1- 3)-BETA-D-GLUCOPYRANOSE'>GXX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GXX:ALPHA-D-XYLOPYRANOSYL-(1- 3)-ALPHA-D-XYLOPYRANOSYL-(1- 3)-BETA-D-GLUCOPYRANOSE'>GXX</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">F9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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_IXa Coagulation factor IXa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.22 3.4.21.22] </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_IXa Coagulation factor IXa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.22 3.4.21.22] </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=5vyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyg OCA], [http://pdbe.org/5vyg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyg RCSB], [http://www.ebi.ac.uk/pdbsum/5vyg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyg 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=5vyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyg OCA], [http://pdbe.org/5vyg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyg RCSB], [http://www.ebi.ac.uk/pdbsum/5vyg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyg ProSAT]</span></td></tr>
Line 12:		Line 13:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN]] Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa.		[[http://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN]] Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glycosylation in the endoplasmic reticulum (ER) is closely associated with protein folding and quality control. We recently described a non-canonical ER quality control mechanism for folding of thrombospondin type 1 repeats by protein O-fucosyltransferase 2 (POFUT2). Epidermal growth factor-like (EGF) repeats are also small cysteine-rich protein motifs that can be O-glycosylated by several ER-localized enzymes, including protein O-glucosyltransferase 1 (POGLUT1) and POFUT1. Both POGLUT1 and POFUT1 modify the Notch receptor on multiple EGF repeats and are essential for full Notch function. The fact that POGLUT1 and POFUT1 can distinguish between folded and unfolded EGF repeats raised the possibility that they participate in a quality control pathway for folding of EGF repeats in proteins such as Notch. Here, we demonstrate that cell-surface expression of endogenous Notch1 in HEK293T cells is dependent on the presence of POGLUT1 and POFUT1 in an additive manner. In vitro unfolding assays reveal that addition of O-glucose or O-fucose stabilizes a single EGF repeat and that addition of both O-glucose and O-fucose enhances stability in an additive manner. Finally, we solved the crystal structure of a single EGF repeat covalently modified by a full O-glucose trisaccharide at 2.2 A resolution. The structure reveals that the glycan fills up a surface groove of the EGF with multiple contacts with the protein, providing a chemical basis for the stabilizing effects of the glycans. Taken together, this work suggests that O-fucose and O-glucose glycans cooperatively stabilize individual EGF repeats through intramolecular interactions, thereby regulating Notch trafficking in cells.
		+
		+	O-Glycosylation modulates the stability of epidermal growth factor-like repeats and thereby regulates Notch trafficking.,Takeuchi H, Yu H, Hao H, Takeuchi M, Ito A, Li H, Haltiwanger RS J Biol Chem. 2017 Sep 22;292(38):15964-15973. doi: 10.1074/jbc.M117.800102. Epub , 2017 Jul 20. PMID:28729422<ref>PMID:28729422</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vyg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 17:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Coagulation factor IXa]]		[[Category: Coagulation factor IXa]]
		+	[[Category: Human]]
	[[Category: Li, H L]]		[[Category: Li, H L]]
	[[Category: Yu, H J]]		[[Category: Yu, H J]]

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

OCA — Sat, 07 Oct 2017 10:56:16 GMT

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

←Older revision

Revision as of 10:56, 7 October 2017

OCA: New page: ==Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide==
OCA — Sat, 07 Oct 2017 10:56:13 GMT

New page: ==Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide== <StructureSection load='5vyg' size='340' side='right' caption='5vyg, resolution 2.20Å' scene...

New page

==Crystal structure of hFA9 EGF repeat with O-glucose trisaccharide==
<StructureSection load='5vyg' size='340' side='right' caption='[[5vyg]], [[Resolution|resolution]] 2.20Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5vyg]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VYG OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VYG FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GXX:ALPHA-D-XYLOPYRANOSYL-(1- 3)-ALPHA-D-XYLOPYRANOSYL-(1- 3)-BETA-D-GLUCOPYRANOSE'>GXX</scene></td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/Coagulation_factor_IXa Coagulation factor IXa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.22 3.4.21.22] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vyg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vyg OCA], [http://pdbe.org/5vyg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vyg RCSB], [http://www.ebi.ac.uk/pdbsum/5vyg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vyg ProSAT]</td></tr>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN]] Defects in F9 are the cause of recessive X-linked hemophilia B (HEMB) [MIM:[http://omim.org/entry/306900 306900]]; also known as Christmas disease.<ref>PMID:8295821</ref> <ref>PMID:2592373</ref> <ref>PMID:2743975</ref> <ref>PMID:6603618</ref> <ref>PMID:3009023</ref> <ref>PMID:3790720</ref> <ref>PMID:3401602</ref> <ref>PMID:3243764</ref> <ref>PMID:2713493</ref> <ref>PMID:2714791</ref> <ref>PMID:2773937</ref> <ref>PMID:2775660</ref> <ref>PMID:2753873</ref> <ref>PMID:2738071</ref> <ref>PMID:2472424</ref> <ref>PMID:2339358</ref> <ref>PMID:2372509</ref> <ref>PMID:2162822</ref> <ref>PMID:1958666</ref> <ref>PMID:1902289</ref> <ref>PMID:1346975</ref> <ref>PMID:1615485</ref> <ref>PMID:8257988</ref> <ref>PMID:8076946</ref> <ref>PMID:8199596</ref> <ref>PMID:7981722</ref> <ref>PMID:8680410</ref> <ref>PMID:9222764</ref> <ref>PMID:9590153</ref> <ref>PMID:9452115</ref> <ref>PMID:9600455</ref> <ref>PMID:10698280</ref> <ref>PMID:10094553</ref> <ref>PMID:11122099</ref> <ref>PMID:12588353</ref> <ref>PMID:12604421</ref> Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide. Defects in F9 are the cause of thrombophilia due to factor IX defect (THPH8) [MIM:[http://omim.org/entry/300807 300807]]. A hemostatic disorder characterized by a tendency to thrombosis.<ref>PMID:19846852</ref>
== Function ==
[[http://www.uniprot.org/uniprot/FA9_HUMAN FA9_HUMAN]] Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa.
== References ==
<references/>
TOC
</StructureSection>
[[Category: Coagulation factor IXa]]
[[Category: Li, H L]]
[[Category: Yu, H J]]
[[Category: Egf repeat]]
[[Category: Glycosylation]]
[[Category: Hydrolase]]
[[Category: Notch regulation]]
[[Category: Transferase]]
[[Category: Transferase-hydrolase complex]]