5xfc - Revision history

OCA at 10:03, 6 September 2023

OCA — Wed, 06 Sep 2023 10:03:24 GMT

←Older revision		Revision as of 10:03, 6 September 2023
Line 1:		Line 1:

	==Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns)==		==Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns)==
-	<StructureSection load='5xfc' size='340' side='right' caption='[[5xfc]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5xfc' size='340' side='right'caption='[[5xfc]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xfc]] is a 2 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=5XFC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XFC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xfc]] is a 2 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=5XFC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XFC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MBE:~~4~~-NITROPHENYL-BETA-D-MANNOPYRANOSIDE'>MBE</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]] 1.4Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MBE:4-NITROPHENYL-BETA-D-MANNOPYRANOSIDE'>MBE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[5xfd\|5xfd]]</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=5xfc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfc OCA], [https://pdbe.org/5xfc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xfc RCSB], [https://www.ebi.ac.uk/pdbsum/5xfc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfc ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">POMGNT1, MGAT1.2, UNQ746/PRO1475 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5xfc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfc OCA], [~~http~~://pdbe.org/5xfc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xfc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xfc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfc ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PMGT1_HUMAN PMGT1_HUMAN]] Walker-Warburg syndrome;Autosomal recessive limb-girdle muscular dystrophy type 2O;Congenital muscular dystrophy with cerebellar involvement;Muscle-eye-brain disease. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/PMGT1_HUMAN PMGT1_HUMAN] Walker-Warburg syndrome;Autosomal recessive limb-girdle muscular dystrophy type 2O;Congenital muscular dystrophy with cerebellar involvement;Muscle-eye-brain disease. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PMGT1_HUMAN PMGT1_HUMAN]] Participates in O-mannosyl glycosylation. May be responsible for the synthesis of the GlcNAc(beta1-2)Man(alpha1-)O-Ser/Thr moiety on alpha-dystroglycan and other O-mannosylated proteins. Is specific for alpha linked terminal mannose and does not have MGAT3, MGAT4, MGAT5, MGAT7 or MGAT8 activity.<ref>PMID:11709191</ref>	+	[https://www.uniprot.org/uniprot/PMGT1_HUMAN PMGT1_HUMAN] Participates in O-mannosyl glycosylation. May be responsible for the synthesis of the GlcNAc(beta1-2)Man(alpha1-)O-Ser/Thr moiety on alpha-dystroglycan and other O-mannosylated proteins. Is specific for alpha linked terminal mannose and does not have MGAT3, MGAT4, MGAT5, MGAT7 or MGAT8 activity.<ref>PMID:11709191</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Fumiaki, Y]]	+	[[Category: Large Structures]]
-	[[Category: Kato, R]]	+	[[Category: Fumiaki Y]]
-	[[Category: Kuwabara, N]]	+	[[Category: Kato R]]
-	[[Category: Manya, H]]	+	[[Category: Kuwabara N]]
-	~~[[Category: Carbohydrate-binding domain]]~~	+	[[Category: Manya H]]
-	~~[[Category: Glycosyltransferase]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 20:51, 24 January 2018

OCA — Wed, 24 Jan 2018 20:51:50 GMT

←Older revision		Revision as of 20:51, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5xfc' size='340' side='right' caption='[[5xfc]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5xfc' size='340' side='right' caption='[[5xfc]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xfc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XFC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xfc]] is a 2 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=5XFC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XFC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MBE:4-NITROPHENYL-BETA-D-MANNOPYRANOSIDE'>MBE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MBE:4-NITROPHENYL-BETA-D-MANNOPYRANOSIDE'>MBE</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xfd\|5xfd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xfd\|5xfd]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POMGNT1, MGAT1.2, UNQ746/PRO1475 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5xfc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfc OCA], [http://pdbe.org/5xfc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xfc RCSB], [http://www.ebi.ac.uk/pdbsum/5xfc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfc 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=5xfc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfc OCA], [http://pdbe.org/5xfc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xfc RCSB], [http://www.ebi.ac.uk/pdbsum/5xfc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfc ProSAT]</span></td></tr>
	</table>		</table>
Line 26:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Fumiaki, Y]]		[[Category: Fumiaki, Y]]
	[[Category: Kato, R]]		[[Category: Kato, R]]

OCA at 07:04, 25 October 2017

OCA — Wed, 25 Oct 2017 07:04:16 GMT

←Older revision		Revision as of 07:04, 25 October 2017
Line 13:		Line 13:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PMGT1_HUMAN PMGT1_HUMAN]] Participates in O-mannosyl glycosylation. May be responsible for the synthesis of the GlcNAc(beta1-2)Man(alpha1-)O-Ser/Thr moiety on alpha-dystroglycan and other O-mannosylated proteins. Is specific for alpha linked terminal mannose and does not have MGAT3, MGAT4, MGAT5, MGAT7 or MGAT8 activity.<ref>PMID:11709191</ref>		[[http://www.uniprot.org/uniprot/PMGT1_HUMAN PMGT1_HUMAN]] Participates in O-mannosyl glycosylation. May be responsible for the synthesis of the GlcNAc(beta1-2)Man(alpha1-)O-Ser/Thr moiety on alpha-dystroglycan and other O-mannosylated proteins. Is specific for alpha linked terminal mannose and does not have MGAT3, MGAT4, MGAT5, MGAT7 or MGAT8 activity.<ref>PMID:11709191</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX. Here, selenomethionine derivatization and mercury soaking have been investigated for SFX experiments using the high-energy XFEL at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA), Hyogo, Japan. Three successful cases are reported of single-wavelength anomalous diffraction (SAD) phasing using X-rays of less than 1 A wavelength with reasonable numbers of diffraction patterns (13 000, 60 000 and 11 000). It is demonstrated that the combination of high-energy X-rays from an XFEL and commonly used heavy-atom incorporation techniques will enable routine de novo structural determination of biomacromolecules.
		+
		+	Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography.,Yamashita K, Kuwabara N, Nakane T, Murai T, Mizohata E, Sugahara M, Pan D, Masuda T, Suzuki M, Sato T, Kodan A, Yamaguchi T, Nango E, Tanaka T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Manya H, Endo T, Kato R, Senda T, Kato H, Iwata S, Ago H, Yamamoto M, Yumoto F, Nakatsu T IUCrJ. 2017 Aug 8;4(Pt 5):639-647. doi: 10.1107/S2052252517008557. eCollection, 2017 Sep 1. PMID:28989719<ref>PMID:28989719</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xfc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:01, 5 September 2017

OCA — Tue, 05 Sep 2017 15:01:06 GMT

←Older revision		Revision as of 15:01, 5 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5xfc is ON HOLD until Paper Publication~~	+	==Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns)==
-		+	<StructureSection load='5xfc' size='340' side='right' caption='[[5xfc]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors: Kuwabara, N., Fumiaki, Y., Kato, R., Manya, H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xfc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XFC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XFC FirstGlance]. <br>
-	~~Description:~~ Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MBE:4-NITROPHENYL-BETA-D-MANNOPYRANOSIDE'>MBE</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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xfd\|5xfd]]</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=5xfc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xfc OCA], [http://pdbe.org/5xfc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xfc RCSB], [http://www.ebi.ac.uk/pdbsum/5xfc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xfc ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PMGT1_HUMAN PMGT1_HUMAN]] Walker-Warburg syndrome;Autosomal recessive limb-girdle muscular dystrophy type 2O;Congenital muscular dystrophy with cerebellar involvement;Muscle-eye-brain disease. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PMGT1_HUMAN PMGT1_HUMAN]] Participates in O-mannosyl glycosylation. May be responsible for the synthesis of the GlcNAc(beta1-2)Man(alpha1-)O-Ser/Thr moiety on alpha-dystroglycan and other O-mannosylated proteins. Is specific for alpha linked terminal mannose and does not have MGAT3, MGAT4, MGAT5, MGAT7 or MGAT8 activity.<ref>PMID:11709191</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fumiaki, Y]]
	[[Category: Kato, R]]		[[Category: Kato, R]]
	[[Category: Kuwabara, N]]		[[Category: Kuwabara, N]]
	[[Category: Manya, H]]		[[Category: Manya, H]]
-	[[Category: ~~Fumiaki, Y~~]]	+	[[Category: Carbohydrate-binding domain]]
		+	[[Category: Glycosyltransferase]]
		+	[[Category: Sugar binding protein]]

OCA at 13:00, 27 April 2017

OCA — Thu, 27 Apr 2017 13:00:54 GMT

←Older revision		Revision as of 13:00, 27 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Kuwabara, N., Fumiaki, Y., Kato, R., Manya, H.		Authors: Kuwabara, N., Fumiaki, Y., Kato, R., Manya, H.

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

OCA — Wed, 19 Apr 2017 12:07:54 GMT

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

←Older revision

Revision as of 12:07, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xfc is ON HOLD Authors: Kuwabara, N., Fumiaki, Y., Kato, R., Manya, H. Description: Serial femtosecond X-ray structure of a stem domain of human O...

OCA — Wed, 19 Apr 2017 12:07:53 GMT

New page: '''Unreleased structure''' The entry 5xfc is ON HOLD Authors: Kuwabara, N., Fumiaki, Y., Kato, R., Manya, H. Description: Serial femtosecond X-ray structure of a stem domain of human O...

New page

'''Unreleased structure'''

The entry 5xfc is ON HOLD

Authors: Kuwabara, N., Fumiaki, Y., Kato, R., Manya, H.

Description: Serial femtosecond X-ray structure of a stem domain of human O-mannose beta-1,2-N-acetylglucosaminyltransferase solved by Se-SAD using XFEL (refined against 13,000 patterns)
[[Category: Unreleased Structures]]
[[Category: Kato, R]]
[[Category: Kuwabara, N]]
[[Category: Manya, H]]
[[Category: Fumiaki, Y]]