4xmd - Revision history

OCA at 10:49, 10 January 2024

OCA — Wed, 10 Jan 2024 10:49:27 GMT

←Older revision		Revision as of 10:49, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xmd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodnius_prolixus Rhodnius prolixus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XMD FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xmd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodnius_prolixus Rhodnius prolixus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XMD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4xmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xmd OCA], [https://pdbe.org/4xmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xmd RCSB], [https://www.ebi.ac.uk/pdbsum/4xmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xmd 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=4xmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xmd OCA], [https://pdbe.org/4xmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xmd RCSB], [https://www.ebi.ac.uk/pdbsum/4xmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xmd ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:42, 26 April 2023

OCA — Wed, 26 Apr 2023 17:42:51 GMT

←Older revision		Revision as of 17:42, 26 April 2023
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	<StructureSection load='4xmd' size='340' side='right'caption='[[4xmd]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4xmd' size='340' side='right'caption='[[4xmd]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xmd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rhopr Rhopr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XMD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XMD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xmd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodnius_prolixus Rhodnius prolixus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XMD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_dismutase Nitrite dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.6.1 1.7.6.1] </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=4xmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xmd OCA], [https://pdbe.org/4xmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xmd RCSB], [https://www.ebi.ac.uk/pdbsum/4xmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xmd 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=4xmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xmd OCA], [~~http~~://pdbe.org/4xmd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xmd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xmd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xmd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NP7_RHOPR NP7_RHOPR]] Converts nitrite as the sole substrate to form nitric oxide gas (NO). NO(2-) serves both as an electron donor and as an electron acceptor. Binds to negatively charged cell surfaces of activated platelets; binds to L-a-phosphatidyl-L-serine (PS)-bearing phospholipid membranes. Once bound on an activated platelet, NP7 releases its stored nitric oxide gas (NO) into the victim's tissues while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also acts as an anticoagulant by blocking coagulation-factor binding sites. Has antihistamine activity; binds histamine with high affinity.<ref>PMID:15170336</ref> <ref>PMID:15598503</ref> <ref>PMID:17428677</ref> <ref>PMID:17958381</ref> <ref>PMID:19655755</ref>	+	[https://www.uniprot.org/uniprot/NP7_RHOPR NP7_RHOPR] Converts nitrite as the sole substrate to form nitric oxide gas (NO). NO(2-) serves both as an electron donor and as an electron acceptor. Binds to negatively charged cell surfaces of activated platelets; binds to L-a-phosphatidyl-L-serine (PS)-bearing phospholipid membranes. Once bound on an activated platelet, NP7 releases its stored nitric oxide gas (NO) into the victim's tissues while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also acts as an anticoagulant by blocking coagulation-factor binding sites. Has antihistamine activity; binds histamine with high affinity.<ref>PMID:15170336</ref> <ref>PMID:15598503</ref> <ref>PMID:17428677</ref> <ref>PMID:17958381</ref> <ref>PMID:19655755</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Nitrite dismutase]]~~	+	[[Category: Rhodnius prolixus]]
-	~~[[Category: Rhopr~~]]	+	[[Category: Ogata H]]
-	[[Category: Ogata, H]]	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: No transpoter]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 07:34, 29 May 2019

OCA — Wed, 29 May 2019 07:34:47 GMT

←Older revision		Revision as of 07:34, 29 May 2019
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	==Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8==		==Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8==
-	<StructureSection load='4xmd' size='340' side='right' caption='[[4xmd]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4xmd' size='340' side='right'caption='[[4xmd]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xmd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XMD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xmd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhopr Rhopr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XMD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_dismutase Nitrite dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.6.1 1.7.6.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_dismutase Nitrite dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.6.1 1.7.6.1] </span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 4xmd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xmd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrophorin\|Nitrophorin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Nitrite dismutase]]		[[Category: Nitrite dismutase]]
		+	[[Category: Rhopr]]
	[[Category: Ogata, H]]		[[Category: Ogata, H]]
	[[Category: Heme]]		[[Category: Heme]]

OCA at 13:28, 4 May 2017

OCA — Thu, 04 May 2017 13:28:26 GMT

←Older revision

Revision as of 13:28, 4 May 2017

OCA at 14:38, 29 July 2015

OCA — Wed, 29 Jul 2015 14:38:01 GMT

←Older revision		Revision as of 14:38, 29 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8==
		+	<StructureSection load='4xmd' size='340' side='right' caption='[[4xmd]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xmd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XMD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_dismutase Nitrite dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.6.1 1.7.6.1] </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=4xmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xmd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xmd RCSB], [http://www.ebi.ac.uk/pdbsum/4xmd PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NP7_RHOPR NP7_RHOPR]] Converts nitrite as the sole substrate to form nitric oxide gas (NO). NO(2-) serves both as an electron donor and as an electron acceptor. Binds to negatively charged cell surfaces of activated platelets; binds to L-a-phosphatidyl-L-serine (PS)-bearing phospholipid membranes. Once bound on an activated platelet, NP7 releases its stored nitric oxide gas (NO) into the victim's tissues while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also acts as an anticoagulant by blocking coagulation-factor binding sites. Has antihistamine activity; binds histamine with high affinity.<ref>PMID:15170336</ref> <ref>PMID:15598503</ref> <ref>PMID:17428677</ref> <ref>PMID:17958381</ref> <ref>PMID:19655755</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

-	~~The entry 4xmd is ON HOLD until Paper Publication~~	+	Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7.,Knipp M, Ogata H, Soavi G, Cerullo G, Allegri A, Abbruzzetti S, Bruno S, Viappiani C, Bidon-Chanal A, Luque FJ F1000Res. 2015 Feb 13;4:45. doi: 10.12688/f1000research.6060.1. eCollection 2015. PMID:26167269<ref>PMID:26167269</ref>

-	~~Authors: Ogata~~, H.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure~~ of ~~nitrophorin 7 from Rhodnius prolixus at pH 7~~.8	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Nitrite dismutase]]
	[[Category: Ogata, H]]		[[Category: Ogata, H]]
		+	[[Category: Heme]]
		+	[[Category: No transpoter]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Transport protein]]

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

OCA — Wed, 21 Jan 2015 16:01:29 GMT

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

←Older revision

Revision as of 16:01, 21 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xmd is ON HOLD until Paper Publication Authors: Ogata, H. Description: Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 [[Categ...

OCA — Wed, 21 Jan 2015 16:01:27 GMT

New page: '''Unreleased structure''' The entry 4xmd is ON HOLD until Paper Publication Authors: Ogata, H. Description: Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8 [[Categ...

New page

'''Unreleased structure'''

The entry 4xmd is ON HOLD until Paper Publication

Authors: Ogata, H.

Description: Crystal structure of nitrophorin 7 from Rhodnius prolixus at pH 7.8
[[Category: Unreleased Structures]]
[[Category: Ogata, H]]