5v8g - Revision history

OCA at 13:43, 4 October 2023

OCA — Wed, 04 Oct 2023 13:43:50 GMT

←Older revision		Revision as of 13:43, 4 October 2023
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	<StructureSection load='5v8g' size='340' side='right'caption='[[5v8g]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='5v8g' size='340' side='right'caption='[[5v8g]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v8g]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Anas_platyrhynchos Anas platyrhynchos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V8G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v8g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Anas_platyrhynchos Anas platyrhynchos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V8G 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=SCN:THIOCYANATE+ION'>SCN</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]] 1.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5v92\|5v92]]~~, ~~[[5v94\|5v94]]~~</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=SCN:THIOCYANATE+ION'>SCN</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=5v8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v8g OCA], [~~http~~://pdbe.org/5v8g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v8g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v8g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v8g 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=5v8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v8g OCA], [https://pdbe.org/5v8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v8g RCSB], [https://www.ebi.ac.uk/pdbsum/5v8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v8g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~U3J0P1_ANAPL U3J0P1_ANAPL]~~] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents.~~[SAAS:SAAS00858876]~~	+	[https://www.uniprot.org/uniprot/LYSC1_ANAPL LYSC1_ANAPL] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Anas platyrhynchos]]		[[Category: Anas platyrhynchos]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Christ, D]]	+	[[Category: Christ D]]
-	[[Category: Langley~~, D B]]~~	+	[[Category: Langley DB]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lysozyme]]~~	+
-	~~[[Category: N-acetylmuramidase~~]]	+

OCA at 08:25, 8 January 2020

OCA — Wed, 08 Jan 2020 08:25:00 GMT

←Older revision		Revision as of 08:25, 8 January 2020
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	==Pekin duck lysozyme isoform I (DEL-I)==		==Pekin duck lysozyme isoform I (DEL-I)==
-	<StructureSection load='5v8g' size='340' side='right' caption='[[5v8g]], [[Resolution\|resolution]] 1.20Å' scene=''>	+	<StructureSection load='5v8g' size='340' side='right'caption='[[5v8g]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v8g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Anas_platyrhynchos Anas platyrhynchos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V8G FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v8g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Anas_platyrhynchos Anas platyrhynchos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V8G FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5v8g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v8g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lysozyme 3D structures\|Lysozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Anas platyrhynchos]]		[[Category: Anas platyrhynchos]]
		+	[[Category: Large Structures]]
	[[Category: Christ, D]]		[[Category: Christ, D]]
	[[Category: Langley, D B]]		[[Category: Langley, D B]]

OCA at 06:27, 9 May 2018

OCA — Wed, 09 May 2018 06:27:49 GMT

←Older revision		Revision as of 06:27, 9 May 2018
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	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Biological chelating molecules called siderophores are~~ used to ~~sequester iron and maintain~~ its ~~ferric state. Bacterial substrate-binding proteins (SBPs)~~ bind ~~iron-siderophore complexes and deliver these complexes~~ to ~~ATP~~-~~binding cassette (ABC) transporters for import into the cytoplasm, where the iron can be transferred from the siderophore to catalytic enzymes~~. ~~In Yersinia pestis~~, ~~the causative agent~~ of ~~plague~~, the ~~Yersinia iron-uptake (Yiu) ABC transporter has~~ been ~~shown to improve iron acquisition under iron-chelated conditions. The Yiu transporter has been proposed to be an iron-siderophore transporter; however,~~ the ~~precise siderophore substrate is unknown~~. ~~Therefore~~, the ~~precise role~~ of the ~~Yiu transporter in Y. pestis survival remains uncharacterized. To better understand the function~~ of the ~~Yiu transporter, the crystal structure of YiuA~~ (~~YPO1310/y2875~~), ~~an SBP which functions to present the iron~~-~~siderophore substrate to~~ the ~~transporter for import into the cytoplasm, was~~ determined~~. The 2.20 and 1.77 A resolution X-ray crystal structures reveal a basic triad binding motif at the YiuA canonical substrate-binding site, indicative~~ of ~~a metal-chelate binding site. Structural alignment and computational docking studies support~~ the ~~function of YiuA in~~ binding ~~chelated metal. Additionally, YiuA contains two mobile helices, helix 5 and helix 10, that undergo 2-3 A shifts across crystal forms and demonstrate structural breathing~~ of ~~the c~~-~~clamp architecture. The flexibility in both c-clamp lobes suggest that YiuA substrate transfer resembles the Venus flytrap mechanism that has been proposed for other SBPs~~.	+	Duck egg lysozyme (DEL) is a widely used model antigen owing to its capacity to bind with differential affinity to anti-chicken egg lysozyme antibodies. However, no structures of DEL have so far been reported, and the situation had been complicated by the presence of multiple isoforms and conflicting reports of primary sequence. Here, the structures of two DEL isoforms from the eggs of the commonly used Pekin duck (Anas platyrhynchos) are reported. Using structural analyses in combination with mass spectrometry, non-ambiguous DEL primary sequences are reported. Furthermore, the structures and sequences determined here enable rationalization of the binding affinity of DEL for well documented landmark anti-lysozyme antibodies.

-	~~The~~ crystal structure of ~~the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal~~.,~~Radka CD~~, ~~Chen~~ D, ~~DeLucas LJ~~, ~~Aller SG~~ Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):~~921~~-~~939~~. doi:, 10.1107/~~S2059798317015236~~. Epub 2017 Oct 26. PMID:~~29095164~~<ref>PMID:~~29095164~~</ref>	+	Structural basis of antigen recognition: crystal structure of duck egg lysozyme.,Langley DB, Crossett B, Schofield P, Jackson J, Zeraati M, Maltby D, Christie M, Burnett D, Brink R, Goodnow C, Christ D Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):910-920. doi:, 10.1107/S2059798317013730. Epub 2017 Oct 25. PMID:29095163<ref>PMID:29095163</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 06:36, 18 April 2018

OCA — Wed, 18 Apr 2018 06:36:58 GMT

←Older revision		Revision as of 06:36, 18 April 2018
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/U3J0P1_ANAPL U3J0P1_ANAPL]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents.[SAAS:SAAS00858876]		[[http://www.uniprot.org/uniprot/U3J0P1_ANAPL U3J0P1_ANAPL]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents.[SAAS:SAAS00858876]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biological chelating molecules called siderophores are used to sequester iron and maintain its ferric state. Bacterial substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver these complexes to ATP-binding cassette (ABC) transporters for import into the cytoplasm, where the iron can be transferred from the siderophore to catalytic enzymes. In Yersinia pestis, the causative agent of plague, the Yersinia iron-uptake (Yiu) ABC transporter has been shown to improve iron acquisition under iron-chelated conditions. The Yiu transporter has been proposed to be an iron-siderophore transporter; however, the precise siderophore substrate is unknown. Therefore, the precise role of the Yiu transporter in Y. pestis survival remains uncharacterized. To better understand the function of the Yiu transporter, the crystal structure of YiuA (YPO1310/y2875), an SBP which functions to present the iron-siderophore substrate to the transporter for import into the cytoplasm, was determined. The 2.20 and 1.77 A resolution X-ray crystal structures reveal a basic triad binding motif at the YiuA canonical substrate-binding site, indicative of a metal-chelate binding site. Structural alignment and computational docking studies support the function of YiuA in binding chelated metal. Additionally, YiuA contains two mobile helices, helix 5 and helix 10, that undergo 2-3 A shifts across crystal forms and demonstrate structural breathing of the c-clamp architecture. The flexibility in both c-clamp lobes suggest that YiuA substrate transfer resembles the Venus flytrap mechanism that has been proposed for other SBPs.
		+
		+	The crystal structure of the Yersinia pestis iron chaperone YiuA reveals a basic triad binding motif for the chelated metal.,Radka CD, Chen D, DeLucas LJ, Aller SG Acta Crystallogr D Struct Biol. 2017 Nov 1;73(Pt 11):921-939. doi:, 10.1107/S2059798317015236. Epub 2017 Oct 26. PMID:29095164<ref>PMID:29095164</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5v8g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:31, 15 November 2017

OCA — Wed, 15 Nov 2017 07:31:43 GMT

←Older revision		Revision as of 07:31, 15 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5v8g is ~~ON HOLD until Paper Publication~~	+	==Pekin duck lysozyme isoform I (DEL-I)==
-		+	<StructureSection load='5v8g' size='340' side='right' caption='[[5v8g]], [[Resolution\|resolution]] 1.20Å' scene=''>
-	~~Authors~~: ~~Langley~~, D.B., ~~Christ~~, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5v8g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Anas_platyrhynchos Anas platyrhynchos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V8G FirstGlance]. <br>
-	~~Description~~: ~~Pekin duck lysozyme isoform I (DEL~~-I)	+	</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=SCN:THIOCYANATE+ION'>SCN</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v92\|5v92]], [[5v94\|5v94]]</td></tr>
-	[[Category: ~~Langley, D.B~~]]	+	<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=5v8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v8g OCA], [http://pdbe.org/5v8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v8g RCSB], [http://www.ebi.ac.uk/pdbsum/5v8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v8g ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/U3J0P1_ANAPL U3J0P1_ANAPL]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents.[SAAS:SAAS00858876]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Anas platyrhynchos]]
	[[Category: Christ, D]]		[[Category: Christ, D]]
		+	[[Category: Langley, D B]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lysozyme]]
		+	[[Category: N-acetylmuramidase]]

OCA at 13:56, 27 September 2017

OCA — Wed, 27 Sep 2017 13:56:19 GMT

←Older revision		Revision as of 13:56, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5v8g is ON HOLD	+	The entry 5v8g is ON HOLD until Paper Publication

	Authors: Langley, D.B., Christ, D.		Authors: Langley, D.B., Christ, D.

OCA at 10:50, 10 May 2017

OCA — Wed, 10 May 2017 10:50:56 GMT

←Older revision		Revision as of 10:50, 10 May 2017
Line 3:		Line 3:
	The entry 5v8g is ON HOLD		The entry 5v8g is ON HOLD

-	Authors: Langley, D.B, Christ, D.	+	Authors: Langley, D.B., Christ, D.

	Description: Pekin duck lysozyme isoform I (DEL-I)		Description: Pekin duck lysozyme isoform I (DEL-I)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Langley, D.B, Christ, D]]	+	[[Category: Langley, D.B]]
		+	[[Category: Christ, D]]

OCA: Protected "5v8g" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 11:44:22 GMT

Protected "5v8g" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:44, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v8g is ON HOLD Authors: Langley, D.B, Christ, D. Description: Pekin duck lysozyme isoform I (DEL-I) Category: Unreleased Structures [[Category...

OCA — Wed, 05 Apr 2017 11:44:21 GMT

New page: '''Unreleased structure''' The entry 5v8g is ON HOLD Authors: Langley, D.B, Christ, D. Description: Pekin duck lysozyme isoform I (DEL-I) Category: Unreleased Structures [[Category...

New page

'''Unreleased structure'''

The entry 5v8g is ON HOLD

Authors: Langley, D.B, Christ, D.

Description: Pekin duck lysozyme isoform I (DEL-I)
[[Category: Unreleased Structures]]
[[Category: Langley, D.B, Christ, D]]