1yhu - Revision history

OCA at 08:03, 15 May 2024

OCA — Wed, 15 May 2024 08:03:29 GMT

←Older revision		Revision as of 08:03, 15 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. The March 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Erythrocruorin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_3 10.2210/rcsb_pdb/mom_2013_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YHU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. The March 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Erythrocruorin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_3 10.2210/rcsb_pdb/mom_2013_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YHU 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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.15Å</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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [https://pdbe.org/1yhu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [https://www.ebi.ac.uk/pdbsum/1yhu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yhu 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=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [https://pdbe.org/1yhu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [https://www.ebi.ac.uk/pdbsum/1yhu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yhu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8IFK4_RIFPA Q8IFK4_RIFPA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Riftia pachyptila]]		[[Category: Riftia pachyptila]]
-	[[Category: Carney~~, S L~~]]	+	[[Category: Carney SL]]
-	[[Category: Fisher~~, C R~~]]	+	[[Category: Fisher CR]]
-	[[Category: Flores~~, J F~~]]	+	[[Category: Flores JF]]
-	[[Category: Freytag~~, J K~~]]	+	[[Category: Freytag JK]]
-	[[Category: Green~~, B N~~]]	+	[[Category: Green BN]]
-	[[Category: Royer~~, W E~~]]	+	[[Category: Royer WE]]
-	[[Category: Schaeffer~~, S W]]~~	+	[[Category: Schaeffer SW]]
-	~~[[Category: Globin fold]]~~	+
-	~~[[Category: Hemoglobin]]~~	+
-	~~[[Category: Oxygen storage-transport complex~~]]	+

OCA at 16:28, 3 November 2021

OCA — Wed, 03 Nov 2021 16:28:32 GMT

←Older revision		Revision as of 16:28, 3 November 2021
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	<StructureSection load='1yhu' size='340' side='right'caption='[[1yhu]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='1yhu' size='340' side='right'caption='[[1yhu]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. The March 2013 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Erythrocruorin'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2013_3 10.2210/rcsb_pdb/mom_2013_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YHU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. The March 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Erythrocruorin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_3 10.2210/rcsb_pdb/mom_2013_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YHU 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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [~~http~~://pdbe.org/1yhu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yhu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yhu 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=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [https://pdbe.org/1yhu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [https://www.ebi.ac.uk/pdbsum/1yhu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yhu ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 16:38, 29 January 2020

OCA — Wed, 29 Jan 2020 16:38:01 GMT

←Older revision		Revision as of 16:38, 29 January 2020
Line 1:		Line 1:

	==Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.==		==Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.==
-	<StructureSection load='1yhu' size='340' side='right' caption='[[1yhu]], [[Resolution\|resolution]] 3.15Å' scene=''>	+	<StructureSection load='1yhu' size='340' side='right'caption='[[1yhu]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. The March 2013 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Erythrocruorin'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2013_3 10.2210/rcsb_pdb/mom_2013_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. The March 2013 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Erythrocruorin'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2013_3 10.2210/rcsb_pdb/mom_2013_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHU FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Erythrocruorin]]		[[Category: Erythrocruorin]]
		+	[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Riftia pachyptila]]		[[Category: Riftia pachyptila]]

OCA at 06:25, 25 April 2018

OCA — Wed, 25 Apr 2018 06:25:07 GMT

←Older revision		Revision as of 06:25, 25 April 2018
Line 1:		Line 1:
		+
	==Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.==		==Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.==
	<StructureSection load='1yhu' size='340' side='right' caption='[[1yhu]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='1yhu' size='340' side='right' caption='[[1yhu]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. The March 2013 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Erythrocruorin'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2013_3 10.2210/rcsb_pdb/mom_2013_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHU 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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [http://pdbe.org/1yhu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [http://www.ebi.ac.uk/pdbsum/1yhu PDBsum]</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=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [http://pdbe.org/1yhu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [http://www.ebi.ac.uk/pdbsum/1yhu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yhu ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 10:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yh/1yhu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yh/1yhu_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yhu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Erythrocruorin]]
		+	[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Riftia pachyptila]]		[[Category: Riftia pachyptila]]
	[[Category: Carney, S L]]		[[Category: Carney, S L]]

OCA at 23:37, 11 September 2015

OCA — Fri, 11 Sep 2015 23:37:14 GMT

←Older revision		Revision as of 23:37, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHU 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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [http://www.ebi.ac.uk/pdbsum/1yhu PDBsum]</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=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [http://pdbe.org/1yhu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [http://www.ebi.ac.uk/pdbsum/1yhu PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	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>
	</div>		</div>
		+	<div class="pdbe-citations 1yhu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 08:54, 8 January 2015

OCA — Thu, 08 Jan 2015 08:54:13 GMT

←Older revision		Revision as of 08:54, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [http://www.ebi.ac.uk/pdbsum/1yhu PDBsum]</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=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [http://www.ebi.ac.uk/pdbsum/1yhu PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Riftia pachyptila]]		[[Category: Riftia pachyptila]]
-	[[Category: Carney, S L.]]	+	[[Category: Carney, S L]]
-	[[Category: Fisher, C R.]]	+	[[Category: Fisher, C R]]
-	[[Category: Flores, J F.]]	+	[[Category: Flores, J F]]
-	[[Category: Freytag, J K.]]	+	[[Category: Freytag, J K]]
-	[[Category: Green, B N.]]	+	[[Category: Green, B N]]
-	[[Category: Royer, W E.]]	+	[[Category: Royer, W E]]
-	[[Category: Schaeffer, S W.]]	+	[[Category: Schaeffer, S W]]
	[[Category: Globin fold]]		[[Category: Globin fold]]
	[[Category: Hemoglobin]]		[[Category: Hemoglobin]]
	[[Category: Oxygen storage-transport complex]]		[[Category: Oxygen storage-transport complex]]

OCA at 20:18, 29 September 2014

OCA — Mon, 29 Sep 2014 20:18:33 GMT

←Older revision		Revision as of 20:18, 29 September 2014
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-	[[~~Image~~:1yhu.~~png\|left~~\|200px]]	+	==Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.==
		+	<StructureSection load='1yhu' size='340' side='right' caption='[[1yhu]], [[Resolution\|resolution]] 3.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YHU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yhu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yhu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yhu RCSB], [http://www.ebi.ac.uk/pdbsum/1yhu PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yh/1yhu_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Key to the remarkable ability of vestimentiferan tubeworms to thrive in the harsh conditions of hydrothermal vents are hemoglobins that permit the sequestration and delivery of hydrogen sulfide and oxygen to chemoautotrophic bacteria. Here, we demonstrate that zinc ions, not free cysteine residues, bind sulfide in vestimentiferan hemoglobins. The crystal structure of the C1 hemoglobin from the hydrothermal vent tubeworm Riftia pachyptila has been determined to 3.15 A and revealed the unexpected presence of 12 tightly bound Zn(2+) ions near the threefold axes of this D(3) symmetric hollow sphere. Chelation experiments on R. pachyptila whole-coelomic fluid and purified hemoglobins reveal a role for Zn(2+) ions in sulfide binding. Free cysteine residues, previously proposed as sulfide-binding sites in vestimentiferan hemoglobins, are found buried in surprisingly hydrophobic pockets below the surface of the R. pachyptila C1 molecule, suggesting that access of these residues to environmental sulfide is restricted. Attempts to reduce the sulfide-binding capacities of R. pachyptila hemoglobins by addition of a thiol inhibitor were also unsuccessful. These findings challenge the currently accepted paradigm of annelid hemoglobin evolution and adaptation to reducing environments.

-	~~{{STRUCTURE_1yhu\| PDB=1yhu \| SCENE= }}~~	+	Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin.,Flores JF, Fisher CR, Carney SL, Green BN, Freytag JK, Schaeffer SW, Royer WE Jr Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2713-8. Epub 2005 Feb 14. PMID:15710902<ref>PMID:15710902</ref>

-	~~===Crystal structure~~ of ~~Riftia pachyptila C1 hemoglobin reveals novel assembly~~ of ~~24 subunits~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15710902}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1yhu]] is a 24 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA].~~	+

	==See Also==		==See Also==
-	*[[Hemoglobin\|Hemoglobin]]	+	*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015710902<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Riftia pachyptila]]		[[Category: Riftia pachyptila]]
	[[Category: Carney, S L.]]		[[Category: Carney, S L.]]

OCA at 21:31, 20 October 2012

OCA — Sat, 20 Oct 2012 21:31:25 GMT

←Older revision		Revision as of 21:31, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[1yhu]] is a 24 chain structure ~~of [[Hemoglobin]]~~ with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA].	+	[[1yhu]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA].

	==See Also==		==See Also==

OCA: Protected "1yhu" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 13:30:56 GMT

Protected "1yhu" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:30, 27 July 2012

OCA at 13:30, 27 July 2012

OCA — Fri, 27 Jul 2012 13:30:55 GMT

←Older revision		Revision as of 13:30, 27 July 2012
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-	{{Seed}}
	[[Image:1yhu.png\|left\|200px]]		[[Image:1yhu.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yhu", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-	-->
	{{STRUCTURE_1yhu\| PDB=1yhu \| SCENE= }}		{{STRUCTURE_1yhu\| PDB=1yhu \| SCENE= }}

	===Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.===		===Crystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15710902}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15710902 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15710902}}		{{ABSTRACT_PUBMED_15710902}}

	==About this Structure==		==About this Structure==
-	~~1YHU~~ is a 24 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA].	+	[[1yhu]] is a 24 chain structure of [[Hemoglobin]] with sequence from [http://en.wikipedia.org/wiki/Riftia_pachyptila Riftia pachyptila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YHU OCA].
		+
		+	==See Also==
		+	*[[Hemoglobin\|Hemoglobin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15710902~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015710902</ref><references group="xtra"/>
	[[Category: Riftia pachyptila]]		[[Category: Riftia pachyptila]]
	[[Category: Carney, S L.]]		[[Category: Carney, S L.]]
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	[[Category: Globin fold]]		[[Category: Globin fold]]
	[[Category: Hemoglobin]]		[[Category: Hemoglobin]]
-		+	[[Category: Oxygen storage-transport complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 06:56:33 2009''~~	+