4x08 - Revision history

OCA at 10:45, 10 January 2024

OCA — Wed, 10 Jan 2024 10:45:39 GMT

←Older revision		Revision as of 10:45, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x08]] 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=4X08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X08 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x08]] 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=4X08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X08 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.34Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4x08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x08 OCA], [https://pdbe.org/4x08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x08 RCSB], [https://www.ebi.ac.uk/pdbsum/4x08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x08 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=4x08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x08 OCA], [https://pdbe.org/4x08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x08 RCSB], [https://www.ebi.ac.uk/pdbsum/4x08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x08 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:05, 12 April 2023

OCA — Wed, 12 Apr 2023 21:05:35 GMT

←Older revision		Revision as of 21:05, 12 April 2023
Line 3:		Line 3:
	<StructureSection load='4x08' size='340' side='right'caption='[[4x08]], [[Resolution\|resolution]] 1.34Å' scene=''>		<StructureSection load='4x08' size='340' side='right'caption='[[4x08]], [[Resolution\|resolution]] 1.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x08]] 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=4X08 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X08 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x08]] 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=4X08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X08 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4a2o\|4a2o]], [[4oxb\|4oxb]]</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=4x08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x08 OCA], [https://pdbe.org/4x08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x08 RCSB], [https://www.ebi.ac.uk/pdbsum/4x08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x08 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNASE3, ECP, RNS3 ([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=4x08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x08 OCA], [~~http~~://pdbe.org/4x08 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x08 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x08 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x08 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ECP_HUMAN ECP_HUMAN]] Cytotoxin and helminthotoxin with low-efficiency ribonuclease activity. Possesses a wide variety of biological activities. Exhibits antibacterial activity, including cytoplasmic membrane depolarization of preferentially Gram-negative, but also Gram-positive strains. Promotes E.coli outer membrane detachment, alteration of the overall cell shape and partial loss of cell content.<ref>PMID:2501794</ref> <ref>PMID:19450231</ref>	+	[https://www.uniprot.org/uniprot/ECP_HUMAN ECP_HUMAN] Cytotoxin and helminthotoxin with low-efficiency ribonuclease activity. Possesses a wide variety of biological activities. Exhibits antibacterial activity, including cytoplasmic membrane depolarization of preferentially Gram-negative, but also Gram-positive strains. Promotes E.coli outer membrane detachment, alteration of the overall cell shape and partial loss of cell content.<ref>PMID:2501794</ref> <ref>PMID:19450231</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The human eosinophil cationic protein (ECP), also known as RNase 3, is an eosinophil secretion protein that is involved in innate immunity and displays antipathogen and proinflammatory activities. ECP has a high binding affinity for heterosaccharides, such as bacterial lipopolysaccharides and heparan sulfate found in the glycocalix of eukaryotic cells. We have crystallized ECP in complex with sulfate anions in a new monoclinic crystal form. In this form, the active site groove is exposed, providing an alternative model for ligand binding studies. By exploring the protein-sulfate complex, we have defined the sulfate binding site architecture. Three main sites (S1-S3) are located in the protein active site; S1 and S2 overlap with the phosphate binding sites involved in RNase nucleotide recognition. A new site (S3) that is unique to ECP is one of the key anchoring points for sulfated ligands. Arg 1 and Arg 7 in S3, together with Arg 34 and Arg 36 in S1, form the main basic clusters that assist in the recognition of ligand anionic groups. The location of additional sulfate bound molecules, some of which contribute to the crystal packing, may mimic the binding to extended anionic polymers. In conclusion, the structural data define a binding pattern for the recognition of sulfated molecules that can modulate the role of ECP in innate immunity. The results reveal the structural basis for the high affinity of ECP for glycosaminoglycans and can assist in structure-based drug design of inhibitors of the protein cytotoxicity to host tissues during inflammation.	+
-		+
-	The sulfate-binding site structure of the human eosinophil cationic protein as revealed by a new crystal form.,Boix E, Pulido D, Moussaoui M, Victoria Nogues M, Russi S J Struct Biol. 2012 Jul;179(1):1-9. Epub 2012 May 9. PMID:22579681<ref>PMID:22579681</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4x08" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blanco~~, J A~~]]	+	[[Category: Blanco JA]]
-	[[Category: Boix, E]]	+	[[Category: Boix E]]
-	[[Category: Garcia~~, J M~~]]	+	[[Category: Garcia JM]]
-	[[Category: Moussauoi, M]]	+	[[Category: Moussauoi M]]
-	[[Category: Salazar~~, V A~~]]	+	[[Category: Salazar VA]]
-	[[Category: Sanchez, D]]	+	[[Category: Sanchez D]]
-	~~[[Category: Active centre mutation]]~~	+
-	~~[[Category: Ecp]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Sulphate]]~~	+
-	~~[[Category: Sulphate recognition site~~]]	+

OCA at 08:44, 23 May 2019

OCA — Thu, 23 May 2019 08:44:10 GMT

←Older revision		Revision as of 08:44, 23 May 2019
Line 1:		Line 1:
		+
	==Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.==		==Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.==
-	<StructureSection load='4x08' size='340' side='right' caption='[[4x08]], [[Resolution\|resolution]] 1.34Å' scene=''>	+	<StructureSection load='4x08' size='340' side='right'caption='[[4x08]], [[Resolution\|resolution]] 1.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X08 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X08 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x08]] 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=4X08 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X08 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4a2o\|4a2o]], [[4oxb\|4oxb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4a2o\|4a2o]], [[4oxb\|4oxb]]</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=4x08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x08 OCA], [http://pdbe.org/4x08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x08 RCSB], [http://www.ebi.ac.uk/pdbsum/4x08 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RNASE3, ECP, RNS3 ([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=4x08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x08 OCA], [http://pdbe.org/4x08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x08 RCSB], [http://www.ebi.ac.uk/pdbsum/4x08 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x08 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Blanco, J A]]		[[Category: Blanco, J A]]
	[[Category: Boix, E]]		[[Category: Boix, E]]

OCA at 13:43, 7 October 2015

OCA — Wed, 07 Oct 2015 13:43:16 GMT

←Older revision		Revision as of 13:43, 7 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.==
		+	<StructureSection load='4x08' size='340' side='right' caption='[[4x08]], [[Resolution\|resolution]] 1.34Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4x08]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X08 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X08 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4a2o\|4a2o]], [[4oxb\|4oxb]]</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=4x08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x08 OCA], [http://pdbe.org/4x08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x08 RCSB], [http://www.ebi.ac.uk/pdbsum/4x08 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ECP_HUMAN ECP_HUMAN]] Cytotoxin and helminthotoxin with low-efficiency ribonuclease activity. Possesses a wide variety of biological activities. Exhibits antibacterial activity, including cytoplasmic membrane depolarization of preferentially Gram-negative, but also Gram-positive strains. Promotes E.coli outer membrane detachment, alteration of the overall cell shape and partial loss of cell content.<ref>PMID:2501794</ref> <ref>PMID:19450231</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human eosinophil cationic protein (ECP), also known as RNase 3, is an eosinophil secretion protein that is involved in innate immunity and displays antipathogen and proinflammatory activities. ECP has a high binding affinity for heterosaccharides, such as bacterial lipopolysaccharides and heparan sulfate found in the glycocalix of eukaryotic cells. We have crystallized ECP in complex with sulfate anions in a new monoclinic crystal form. In this form, the active site groove is exposed, providing an alternative model for ligand binding studies. By exploring the protein-sulfate complex, we have defined the sulfate binding site architecture. Three main sites (S1-S3) are located in the protein active site; S1 and S2 overlap with the phosphate binding sites involved in RNase nucleotide recognition. A new site (S3) that is unique to ECP is one of the key anchoring points for sulfated ligands. Arg 1 and Arg 7 in S3, together with Arg 34 and Arg 36 in S1, form the main basic clusters that assist in the recognition of ligand anionic groups. The location of additional sulfate bound molecules, some of which contribute to the crystal packing, may mimic the binding to extended anionic polymers. In conclusion, the structural data define a binding pattern for the recognition of sulfated molecules that can modulate the role of ECP in innate immunity. The results reveal the structural basis for the high affinity of ECP for glycosaminoglycans and can assist in structure-based drug design of inhibitors of the protein cytotoxicity to host tissues during inflammation.

-	The ~~entry 4x08 is ON HOLD until Paper Publication~~	+	The sulfate-binding site structure of the human eosinophil cationic protein as revealed by a new crystal form.,Boix E, Pulido D, Moussaoui M, Victoria Nogues M, Russi S J Struct Biol. 2012 Jul;179(1):1-9. Epub 2012 May 9. PMID:22579681<ref>PMID:22579681</ref>

-	~~Authors: Blanco~~, J.A.~~, Garcia, J.M., Salazar, V.A., Sanchez, D., Moussauoi, M., Boix, E~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of H128N~~/~~ECP mutant in complex with sulphate anions at 1.34 Angstroms.~~	+	<div class="pdbe-citations 4x08" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: Garcia, J.M]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Blanco, J A]]
		+	[[Category: Boix, E]]
		+	[[Category: Garcia, J M]]
	[[Category: Moussauoi, M]]		[[Category: Moussauoi, M]]
-	[[Category: ~~Blanco~~, J.A]]	+	[[Category: Salazar, V A]]
-	~~[[Category: Boix, E~~]]	+
	[[Category: Sanchez, D]]		[[Category: Sanchez, D]]
-	[[Category: ~~Salazar, V.A~~]]	+	[[Category: Active centre mutation]]
		+	[[Category: Ecp]]
		+	[[Category: Hydrolase]]
		+	[[Category: Sulphate]]
		+	[[Category: Sulphate recognition site]]

OCA at 20:17, 24 December 2014

OCA — Wed, 24 Dec 2014 20:17:11 GMT

←Older revision		Revision as of 20:17, 24 December 2014
Line 6:		Line 6:

	Description: Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.		Description: Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.
		+	[[Category: Unreleased Structures]]
		+	[[Category: Garcia, J.M]]
		+	[[Category: Moussauoi, M]]
		+	[[Category: Blanco, J.A]]
		+	[[Category: Boix, E]]
		+	[[Category: Sanchez, D]]
		+	[[Category: Salazar, V.A]]

OCA at 08:43, 3 December 2014

OCA — Wed, 03 Dec 2014 08:43:37 GMT

←Older revision		Revision as of 08:43, 3 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4x08 is ON HOLD	+	The entry 4x08 is ON HOLD until Paper Publication

-	Authors: Blanco, J. A., Garcia, J. M., Salazar, V. A., Sanchez, D., Moussauoi, M.	+	Authors: Blanco, J.A., Garcia, J.M., Salazar, V.A., Sanchez, D., Moussauoi, M., Boix, E.

	Description: Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.		Description: Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.

OCA: Protected "4x08" [edit=sysop:move=sysop]

OCA — Wed, 26 Nov 2014 07:15:35 GMT

Protected "4x08" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:15, 26 November 2014

OCA: New page: '''Unreleased structure''' The entry 4x08 is ON HOLD Authors: Blanco, J. A., Garcia, J. M., Salazar, V. A., Sanchez, D., Moussauoi, M. Description: Structure of H128N/ECP mutant in com...

OCA — Wed, 26 Nov 2014 07:15:34 GMT

New page: '''Unreleased structure''' The entry 4x08 is ON HOLD Authors: Blanco, J. A., Garcia, J. M., Salazar, V. A., Sanchez, D., Moussauoi, M. Description: Structure of H128N/ECP mutant in com...

New page

'''Unreleased structure'''

The entry 4x08 is ON HOLD

Authors: Blanco, J. A., Garcia, J. M., Salazar, V. A., Sanchez, D., Moussauoi, M.

Description: Structure of H128N/ECP mutant in complex with sulphate anions at 1.34 Angstroms.