5yy4 - Revision history

OCA at 08:40, 22 November 2023

2023-11-22T08:40:02Z

←Older revision		Revision as of 08:40, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5yy4' size='340' side='right'caption='[[5yy4]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='5yy4' size='340' side='right'caption='[[5yy4]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yy4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YY4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yy4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YY4 FirstGlance]. <br>
-	</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=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]] 1.59Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</scene></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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5yy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy4 OCA], [~~http~~://pdbe.org/5yy4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yy4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yy4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy4 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=5yy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy4 OCA], [https://pdbe.org/5yy4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yy4 RCSB], [https://www.ebi.ac.uk/pdbsum/5yy4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy4 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/CCR5_HUMAN CCR5_HUMAN]] Genetic variation in CCR5 is associated with susceptibility to diabetes mellitus insulin-dependent type 22 (IDDM22) [MIM:[~~http~~://omim.org/entry/612522 612522]]. A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels.<ref>PMID:19073967</ref>	+	[https://www.uniprot.org/uniprot/CCR5_HUMAN CCR5_HUMAN] Genetic variation in CCR5 is associated with susceptibility to diabetes mellitus insulin-dependent type 22 (IDDM22) [MIM:[https://omim.org/entry/612522 612522]. A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels.<ref>PMID:19073967</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CCR5_HUMAN CCR5_HUMAN]] Receptor for a number of inflammatory CC-chemokines including MIP-1-alpha, MIP-1-beta and RANTES and subsequently transduces a signal by increasing the intracellular calcium ion level. May play a role in the control of granulocytic lineage proliferation or differentiation. Acts as a coreceptor (CD4 being the primary receptor) for HIV-1 R5 isolates.<ref>PMID:8639485</ref> <ref>PMID:8663314</ref> <ref>PMID:8699119</ref> <ref>PMID:8649511</ref> <ref>PMID:8649512</ref> <ref>PMID:11323418</ref>	+	[https://www.uniprot.org/uniprot/CCR5_HUMAN CCR5_HUMAN] Receptor for a number of inflammatory CC-chemokines including MIP-1-alpha, MIP-1-beta and RANTES and subsequently transduces a signal by increasing the intracellular calcium ion level. May play a role in the control of granulocytic lineage proliferation or differentiation. Acts as a coreceptor (CD4 being the primary receptor) for HIV-1 R5 isolates.<ref>PMID:8639485</ref> <ref>PMID:8663314</ref> <ref>PMID:8699119</ref> <ref>PMID:8649511</ref> <ref>PMID:8649512</ref> <ref>PMID:11323418</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Caaveiro~~, J M.M~~]]	+	[[Category: Caaveiro JMM]]
-	[[Category: Miyanabe, K]]	+	[[Category: Miyanabe K]]
-	[[Category: Tsumoto, K]]	+	[[Category: Tsumoto K]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Biomolecular recognition]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Md simulation]]~~	+
-	~~[[Category: Thermodynamic~~]]	+

OCA at 09:30, 21 October 2020

2020-10-21T09:30:58Z

←Older revision		Revision as of 09:30, 21 October 2020
Line 1:		Line 1:

	==Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide==		==Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide==
-	<StructureSection load='5yy4' size='340' side='right' caption='[[5yy4]], [[Resolution\|resolution]] 1.59Å' scene=''>	+	<StructureSection load='5yy4' size='340' side='right'caption='[[5yy4]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yy4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YY4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yy4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YY4 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=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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</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=5yy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy4 OCA], [http://pdbe.org/5yy4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yy4 RCSB], [http://www.ebi.ac.uk/pdbsum/5yy4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy4 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5yy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy4 OCA], [http://pdbe.org/5yy4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yy4 RCSB], [http://www.ebi.ac.uk/pdbsum/5yy4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy4 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5yy4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yy4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Caaveiro, J M.M]]		[[Category: Caaveiro, J M.M]]

OCA at 07:31, 25 July 2018

2018-07-25T07:31:23Z

←Older revision		Revision as of 07:31, 25 July 2018
Line 3:		Line 3:
	<StructureSection load='5yy4' size='340' side='right' caption='[[5yy4]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='5yy4' size='340' side='right' caption='[[5yy4]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yy4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YY4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yy4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YY4 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=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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</scene></td></tr>
Line 12:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CCR5_HUMAN CCR5_HUMAN]] Receptor for a number of inflammatory CC-chemokines including MIP-1-alpha, MIP-1-beta and RANTES and subsequently transduces a signal by increasing the intracellular calcium ion level. May play a role in the control of granulocytic lineage proliferation or differentiation. Acts as a coreceptor (CD4 being the primary receptor) for HIV-1 R5 isolates.<ref>PMID:8639485</ref> <ref>PMID:8663314</ref> <ref>PMID:8699119</ref> <ref>PMID:8649511</ref> <ref>PMID:8649512</ref> <ref>PMID:11323418</ref>		[[http://www.uniprot.org/uniprot/CCR5_HUMAN CCR5_HUMAN]] Receptor for a number of inflammatory CC-chemokines including MIP-1-alpha, MIP-1-beta and RANTES and subsequently transduces a signal by increasing the intracellular calcium ion level. May play a role in the control of granulocytic lineage proliferation or differentiation. Acts as a coreceptor (CD4 being the primary receptor) for HIV-1 R5 isolates.<ref>PMID:8639485</ref> <ref>PMID:8663314</ref> <ref>PMID:8699119</ref> <ref>PMID:8649511</ref> <ref>PMID:8649512</ref> <ref>PMID:11323418</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein tyrosine sulfation (PTS) is a post-translational modification regulating numerous biological events. PTS generally occurs at flexible regions of proteins, enhancing intermolecular interactions between proteins. Because of the high flexibility associated with the regions where PTS is generally encountered, an atomic-level understanding has been difficult to achieve by X-ray crystallography or nuclear magnetic resonance techniques. In this study, we focused on the conformational behavior of a flexible sulfated peptide and its interaction with an antibody. Molecular dynamics simulations and thermodynamic analysis indicated that PTS reduced the main-chain fluctuations upon the appearance of sulfate-mediated intramolecular H-bonds. Collectively, our data suggested that one of the mechanisms by which PTS may enhance protein-protein interactions consists of the limitation of conformational dynamics in the unbound state, thus reducing the loss of entropy upon binding and boosting the affinity for its partner.
		+
		+	Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody.,Miyanabe K, Yamashita T, Abe Y, Akiba H, Takamatsu Y, Nakakido M, Hamakubo T, Ueda T, Caaveiro JMM, Tsumoto K Biochemistry. 2018 Jul 17;57(28):4177-4185. doi: 10.1021/acs.biochem.8b00592., Epub 2018 Jul 5. PMID:29936828<ref>PMID:29936828</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yy4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Caaveiro, J M.M]]		[[Category: Caaveiro, J M.M]]
	[[Category: Miyanabe, K]]		[[Category: Miyanabe, K]]

OCA at 07:31, 18 July 2018

2018-07-18T07:31:37Z

←Older revision		Revision as of 07:31, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yy4 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide==
-		+	<StructureSection load='5yy4' size='340' side='right' caption='[[5yy4]], [[Resolution\|resolution]] 1.59Å' scene=''>
-	~~Authors~~: ~~Caaveiro~~, J.M.M., ~~Miyanabe~~, K., ~~Tsumoto~~, K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yy4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YY4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YY4 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of the ~~scFv antibody 4B08 with sulfated epitope peptide~~	+	</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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</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=5yy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yy4 OCA], [http://pdbe.org/5yy4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yy4 RCSB], [http://www.ebi.ac.uk/pdbsum/5yy4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yy4 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/CCR5_HUMAN CCR5_HUMAN]] Genetic variation in CCR5 is associated with susceptibility to diabetes mellitus insulin-dependent type 22 (IDDM22) [MIM:[http://omim.org/entry/612522 612522]]. A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels.<ref>PMID:19073967</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CCR5_HUMAN CCR5_HUMAN]] Receptor for a number of inflammatory CC-chemokines including MIP-1-alpha, MIP-1-beta and RANTES and subsequently transduces a signal by increasing the intracellular calcium ion level. May play a role in the control of granulocytic lineage proliferation or differentiation. Acts as a coreceptor (CD4 being the primary receptor) for HIV-1 R5 isolates.<ref>PMID:8639485</ref> <ref>PMID:8663314</ref> <ref>PMID:8699119</ref> <ref>PMID:8649511</ref> <ref>PMID:8649512</ref> <ref>PMID:11323418</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Caaveiro, J M.M]]
		+	[[Category: Miyanabe, K]]
	[[Category: Tsumoto, K]]		[[Category: Tsumoto, K]]
-	[[Category: ~~Caaveiro, J.M.M~~]]	+	[[Category: Antibody]]
-	[[Category: ~~Miyanabe, K~~]]	+	[[Category: Biomolecular recognition]]
		+	[[Category: Immune system]]
		+	[[Category: Md simulation]]
		+	[[Category: Thermodynamic]]

OCA at 07:11, 27 December 2017

2017-12-27T07:11:46Z

←Older revision		Revision as of 07:11, 27 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yy4 is ON HOLD	+	The entry 5yy4 is ON HOLD until Paper Publication

	Authors: Caaveiro, J.M.M., Miyanabe, K., Tsumoto, K.		Authors: Caaveiro, J.M.M., Miyanabe, K., Tsumoto, K.

OCA: Protected "5yy4" [edit=sysop:move=sysop]

2017-12-13T05:49:27Z

Protected "5yy4" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:49, 13 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yy4 is ON HOLD Authors: Caaveiro, J.M.M., Miyanabe, K., Tsumoto, K. Description: Crystal structure of the scFv antibody 4B08 with sulfated epitope...

2017-12-13T05:49:26Z

New page: '''Unreleased structure''' The entry 5yy4 is ON HOLD Authors: Caaveiro, J.M.M., Miyanabe, K., Tsumoto, K. Description: Crystal structure of the scFv antibody 4B08 with sulfated epitope...

New page

'''Unreleased structure'''

The entry 5yy4 is ON HOLD

Authors: Caaveiro, J.M.M., Miyanabe, K., Tsumoto, K.

Description: Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide
[[Category: Unreleased Structures]]
[[Category: Tsumoto, K]]
[[Category: Caaveiro, J.M.M]]
[[Category: Miyanabe, K]]