5oxs - Revision history

OCA at 01:27, 28 December 2023

OCA — Thu, 28 Dec 2023 01:27:56 GMT

←Older revision		Revision as of 01:27, 28 December 2023
Line 1:		Line 1:

	==Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R5 oligosaccharide==		==Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R5 oligosaccharide==
-	<StructureSection load='5oxs' size='340' side='right' caption='[[5oxs]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='5oxs' size='340' side='right'caption='[[5oxs]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oxs]] 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=5OXS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oxs]] 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=5OXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OXS 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=K5B:4,7-anhydro-3-deoxy-D-~~manno~~-oct-2-ulosonic+acid'>K5B</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]] 1.65Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5oxr\|5oxr]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=K5B:4,7-anhydro-3-deoxy-D-gluco-oct-2-ulosonic+acid'>K5B</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, COLEC7, PSPD, SFTP4 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5oxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxs OCA], [https://pdbe.org/5oxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oxs RCSB], [https://www.ebi.ac.uk/pdbsum/5oxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxs 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=5oxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxs OCA], [~~http~~://pdbe.org/5oxs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5oxs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5oxs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxs ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.	+	[https://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Greenhough, T J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Shrive, A K~~]]	+	[[Category: Greenhough TJ]]
-	[[Category: ~~Alpha-helical coiled coil]]~~	+	[[Category: Shrive AK]]
-	~~[[Category: Carbohydrate recognition domain]]~~	+
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Neck+crd]]~~	+
-	~~[[Category: Sugar binding protein]]~~	+
-	~~[[Category: Surfactant protein]]~~	+
-	~~[[Category: Trimeric recombinant collectin fragment~~]]	+

OCA at 05:50, 27 June 2018

OCA — Wed, 27 Jun 2018 05:50:04 GMT

←Older revision		Revision as of 05:50, 27 June 2018
Line 3:		Line 3:
	<StructureSection load='5oxs' size='340' side='right' caption='[[5oxs]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='5oxs' size='340' side='right' caption='[[5oxs]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oxs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oxs]] 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=5OXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OXS 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=K5B:4,7-anhydro-3-deoxy-D-manno-oct-2-ulosonic+acid'>K5B</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=K5B:4,7-anhydro-3-deoxy-D-manno-oct-2-ulosonic+acid'>K5B</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5oxr\|5oxr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5oxr\|5oxr]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, COLEC7, PSPD, SFTP4 ([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=5oxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxs OCA], [http://pdbe.org/5oxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oxs RCSB], [http://www.ebi.ac.uk/pdbsum/5oxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxs 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=5oxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxs OCA], [http://pdbe.org/5oxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oxs RCSB], [http://www.ebi.ac.uk/pdbsum/5oxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxs ProSAT]</span></td></tr>
	</table>		</table>
Line 12:		Line 13:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	The ~~carbohydrate recognition domains (CRDs)~~ of ~~lung collectin surfactant protein~~ D (SP-D) ~~recognize sugar patterns on~~ the ~~surface~~ of ~~lung pathogens and promote phagocytosis. Using Haemophilus influenzae Eagan~~ strains ~~expressing well-characterized lipopolysaccharide~~ (~~LPS~~) ~~surface~~ structures ~~of various levels of complexity, we show~~ that ~~bacterial recognition and binding by SP~~-D ~~is inversely related to LPS chain extent~~ and ~~complexity. The crystal structure of a biologically active recombinant trimeric SP~~-~~D CRD complexed~~ with ~~a delipidated Eagan 4A LPS suggests that efficient LPS~~ recognition ~~by SP~~-~~D requires multiple~~ binding interactions ~~utilizing~~ the ~~three major ligand-binding determinants in~~ the ~~SP-D~~ binding ~~pocket,~~ with ~~Ca-dependent~~ binding of inner~~-core heptose accompanied by interaction~~ of ~~anhydro~~-~~Kdo (4,7-anhydro-3-deoxy-d-manno-oct-2-ulosonic acid) with Arg343~~ and ~~Asp325~~. ~~Combined with enzyme-linked immunosorbent assays (ELISAs)~~ and ~~fluorescence-activated cell sorter (FACS)~~ binding ~~analyses, our results show that extended~~ LPS ~~structures previously thought to be~~ targets ~~for collectins are important in shielding the more vulnerable sites in~~ the LPS core~~, revealing a mechanism by which pathogens with complex LPS extensions efficiently evade a first~~-~~line mucosal innate immune defense. The structure~~ also ~~reveals~~ for the ~~first time the dominant form of anhydro~~-Kdo.	+	The crystal structures of a biologically and therapeutically active recombinant homotrimeric fragment of native human SP-D (hSP-D) complexed with the inner core oligosaccharide of the Salmonella enterica sv Minnesota rough strains R5 and R7 (rough mutant chemotypes Rc and Rd1) have been determined. The structures reveal that hSP-D specifically and preferentially targets the LPS inner core via the innermost conserved Hep-Kdo pair with the flexibility for alternative recognition when this preferred epitope is not available for binding. Hep-Kdo binding is achieved through calcium dependent recognition of the heptose dihydroxyethyl side chain coupled with specific interactions between the Kdo and the binding site flanking residues Arg343 and Asp325 with evidence for an extended binding site for LPS inner cores containing multiple Kdo residues. In one subunit of the R5-bound structure this preferred mode of binding is precluded by the crystal lattice and oligosaccharide is bound through the terminal inner core glucose. The structures presented here thus provide unique multiple insights into the recognition and binding of bacterial LPS by hSP-D. Not only is it demonstrated that hSP-D targets the highly conserved LPS proximal inner core Hep-Kdo motif, but also that hSP-D can recognise either terminal or non-terminal sugars and has the flexibility and versatility to adopt alternative strategies for bacterial recognition, utilising alternative LPS epitopes when the preferred inner core Hep-Kdo disaccharide is not available for binding.

-	~~Crystal Structure~~ of ~~a Complex of Surfactant Protein D (SP~~-D~~) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding~~ of ~~Core Structures in SP-D-Resistant Strains~~.,Clark HW, Mackay RM, ~~Deadman ME, Hood DW~~, Madsen J, ~~Moxon ER~~, ~~Townsend JP, Reid KB, Ahmed A, Shaw AJ~~, Greenhough TJ, Shrive AK ~~Infect Immun~~. ~~2016 Apr 22~~;84(5):~~1585-92~~. doi: 10.~~1128~~/~~IAI~~.~~01239-15~~. ~~Print 2016~~, ~~May~~. PMID:~~26953329~~<ref>PMID:~~26953329~~</ref>	+	Structural definition of hSP-D recognition of Salmonella enterica LPS inner core oligosaccharides reveals alternative binding modes for the same LPS.,Littlejohn JR, da Silva RF, Neale WA, Smallcombe CC, Clark HW, Mackay RA, Watson AS, Madsen J, Hood DW, Burns I, Greenhough TJ, Shrive AK PLoS One. 2018 Jun 18;13(6):e0199175. doi: 10.1371/journal.pone.0199175., eCollection 2018. PMID:29912941<ref>PMID:29912941</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>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Greenhough, T J]]		[[Category: Greenhough, T J]]
	[[Category: Shrive, A K]]		[[Category: Shrive, A K]]

OCA at 05:38, 20 June 2018

OCA — Wed, 20 Jun 2018 05:38:58 GMT

←Older revision		Revision as of 05:38, 20 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5oxs is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R5 oligosaccharide==
		+	<StructureSection load='5oxs' size='340' side='right' caption='[[5oxs]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5oxs]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OXS 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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GMH:L-GLYCERO-D-MANNO-HEPTOPYRANOSE'>GMH</scene>, <scene name='pdbligand=K5B:4,7-anhydro-3-deoxy-D-manno-oct-2-ulosonic+acid'>K5B</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5oxr\|5oxr]]</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=5oxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oxs OCA], [http://pdbe.org/5oxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oxs RCSB], [http://www.ebi.ac.uk/pdbsum/5oxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oxs ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The carbohydrate recognition domains (CRDs) of lung collectin surfactant protein D (SP-D) recognize sugar patterns on the surface of lung pathogens and promote phagocytosis. Using Haemophilus influenzae Eagan strains expressing well-characterized lipopolysaccharide (LPS) surface structures of various levels of complexity, we show that bacterial recognition and binding by SP-D is inversely related to LPS chain extent and complexity. The crystal structure of a biologically active recombinant trimeric SP-D CRD complexed with a delipidated Eagan 4A LPS suggests that efficient LPS recognition by SP-D requires multiple binding interactions utilizing the three major ligand-binding determinants in the SP-D binding pocket, with Ca-dependent binding of inner-core heptose accompanied by interaction of anhydro-Kdo (4,7-anhydro-3-deoxy-d-manno-oct-2-ulosonic acid) with Arg343 and Asp325. Combined with enzyme-linked immunosorbent assays (ELISAs) and fluorescence-activated cell sorter (FACS) binding analyses, our results show that extended LPS structures previously thought to be targets for collectins are important in shielding the more vulnerable sites in the LPS core, revealing a mechanism by which pathogens with complex LPS extensions efficiently evade a first-line mucosal innate immune defense. The structure also reveals for the first time the dominant form of anhydro-Kdo.

-	~~Authors: Shrive~~, A~~.K.~~, Greenhough, T.J.	+	Crystal Structure of a Complex of Surfactant Protein D (SP-D) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding of Core Structures in SP-D-Resistant Strains.,Clark HW, Mackay RM, Deadman ME, Hood DW, Madsen J, Moxon ER, Townsend JP, Reid KB, Ahmed A, Shaw AJ, Greenhough TJ, Shrive AK Infect Immun. 2016 Apr 22;84(5):1585-92. doi: 10.1128/IAI.01239-15. Print 2016, May. PMID:26953329<ref>PMID:26953329</ref>

-	~~Description: Crystal structure~~ of ~~human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R5 oligosaccharide~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Shrive, A.K]]	+	<div class="pdbe-citations 5oxs" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Greenhough, T.J~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Greenhough, T J]]
		+	[[Category: Shrive, A K]]
		+	[[Category: Alpha-helical coiled coil]]
		+	[[Category: Carbohydrate recognition domain]]
		+	[[Category: Lectin]]
		+	[[Category: Neck+crd]]
		+	[[Category: Sugar binding protein]]
		+	[[Category: Surfactant protein]]
		+	[[Category: Trimeric recombinant collectin fragment]]

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

OCA — Wed, 27 Sep 2017 12:58:50 GMT

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

←Older revision

Revision as of 12:58, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5oxs is ON HOLD until Paper Publication Authors: Shrive, A.K., Greenhough, T.J. Description: Crystal structure of human lung surfactant protein D t...

OCA — Wed, 27 Sep 2017 12:58:49 GMT

New page: '''Unreleased structure''' The entry 5oxs is ON HOLD until Paper Publication Authors: Shrive, A.K., Greenhough, T.J. Description: Crystal structure of human lung surfactant protein D t...

New page

'''Unreleased structure'''

The entry 5oxs is ON HOLD until Paper Publication

Authors: Shrive, A.K., Greenhough, T.J.

Description: Crystal structure of human lung surfactant protein D trimeric fragment with bound ligand Salmonella enterica Minnesota R5 oligosaccharide
[[Category: Unreleased Structures]]
[[Category: Shrive, A.K]]
[[Category: Greenhough, T.J]]