4yhp - Revision history

OCA at 08:00, 27 September 2023

2023-09-27T08:00:13Z

←Older revision		Revision as of 08:00, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yhp]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YHP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yhp]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YHP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</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]] 2.53Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</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=4yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhp OCA], [https://pdbe.org/4yhp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yhp RCSB], [https://www.ebi.ac.uk/pdbsum/4yhp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhp 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=4yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhp OCA], [https://pdbe.org/4yhp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yhp RCSB], [https://www.ebi.ac.uk/pdbsum/4yhp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhp ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:14, 3 May 2023

2023-05-03T08:14:36Z

←Older revision		Revision as of 08:14, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4yhp' size='340' side='right'caption='[[4yhp]], [[Resolution\|resolution]] 2.53Å' scene=''>		<StructureSection load='4yhp' size='340' side='right'caption='[[4yhp]], [[Resolution\|resolution]] 2.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yhp]] is a 10 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=4YHP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YHP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yhp]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YHP FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yhz\|4yhz]]~~</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=4yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhp OCA], [https://pdbe.org/4yhp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yhp RCSB], [https://www.ebi.ac.uk/pdbsum/4yhp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhp 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=4yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhp OCA], [~~http~~://pdbe.org/4yhp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yhp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yhp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhp ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/H31_HUMAN H31_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dementieva, I S~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Hattori, T~~]]	+	[[Category: Dementieva IS]]
-	[[Category: ~~Koide, S~~]]	+	[[Category: Hattori T]]
-	[[Category: ~~Montano,~~ S P]]	+	[[Category: Koide S]]
-	[[Category: ~~Antibody]]~~	+	[[Category: Montano SP]]
-	~~[[Category: Fab]]~~	+
-	~~[[Category: H3k9me3]]~~	+
-	~~[[Category: Head-to-head dimerization]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 15:52, 11 December 2019

2019-12-11T15:52:36Z

←Older revision		Revision as of 15:52, 11 December 2019
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	<StructureSection load='4yhp' size='340' side='right'caption='[[4yhp]], [[Resolution\|resolution]] 2.53Å' scene=''>		<StructureSection load='4yhp' size='340' side='right'caption='[[4yhp]], [[Resolution\|resolution]] 2.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yhp]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YHP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yhp]] is a 10 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=4YHP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YHP FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yhz\|4yhz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yhz\|4yhz]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Dementieva, I S]]		[[Category: Dementieva, I S]]

OCA at 07:17, 10 July 2019

2019-07-10T07:17:56Z

←Older revision		Revision as of 07:17, 10 July 2019
Line 1:		Line 1:

	==Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide==		==Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide==
-	<StructureSection load='4yhp' size='340' side='right' caption='[[4yhp]], [[Resolution\|resolution]] 2.53Å' scene=''>	+	<StructureSection load='4yhp' size='340' side='right'caption='[[4yhp]], [[Resolution\|resolution]] 2.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yhp]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YHP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yhp]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YHP FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Dementieva, I S]]		[[Category: Dementieva, I S]]
	[[Category: Hattori, T]]		[[Category: Hattori, T]]

OCA at 06:14, 6 October 2017

2017-10-06T06:14:58Z

←Older revision		Revision as of 06:14, 6 October 2017
Line 6:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yhz\|4yhz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yhz\|4yhz]]</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=4yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhp OCA], [http://pdbe.org/4yhp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yhp RCSB], [http://www.ebi.ac.uk/pdbsum/4yhp 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=4yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhp OCA], [http://pdbe.org/4yhp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yhp RCSB], [http://www.ebi.ac.uk/pdbsum/4yhp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:11, 20 February 2016

2016-02-20T19:11:38Z

←Older revision		Revision as of 19:11, 20 February 2016
Line 1:		Line 1:
		+
	==Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide==		==Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide==
	<StructureSection load='4yhp' size='340' side='right' caption='[[4yhp]], [[Resolution\|resolution]] 2.53Å' scene=''>		<StructureSection load='4yhp' size='340' side='right' caption='[[4yhp]], [[Resolution\|resolution]] 2.53Å' scene=''>
Line 7:		Line 8:
	<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=4yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhp OCA], [http://pdbe.org/4yhp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yhp RCSB], [http://www.ebi.ac.uk/pdbsum/4yhp 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=4yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhp OCA], [http://pdbe.org/4yhp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yhp RCSB], [http://www.ebi.ac.uk/pdbsum/4yhp PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. This "antigen clasping" produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody-antigen recognition and suggests a strategy for developing extremely specific antibodies.
		+
		+	Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation.,Hattori T, Lai D, Dementieva IS, Montano SP, Kurosawa K, Zheng Y, Akin LR, Swist-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S Proc Natl Acad Sci U S A. 2016 Feb 9. pii: 201522691. PMID:26862167<ref>PMID:26862167</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4yhp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:23, 10 February 2016

2016-02-10T17:23:15Z

←Older revision		Revision as of 17:23, 10 February 2016
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide==
-		+	<StructureSection load='4yhp' size='340' side='right' caption='[[4yhp]], [[Resolution\|resolution]] 2.53Å' scene=''>
-	~~The entry~~ 4yhp is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4yhp]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YHP FirstGlance]. <br>
-	~~Authors~~: ~~Hattori, T~~., ~~Dementieva, I~~.S., ~~Montano~~, S.P., ~~Koide, S~~.	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4yhz\|4yhz]]</td></tr>
-	~~Description: Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide~~	+	<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=4yhp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhp OCA], [http://pdbe.org/4yhp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yhp RCSB], [http://www.ebi.ac.uk/pdbsum/4yhp PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dementieva, I S]]
	[[Category: Hattori, T]]		[[Category: Hattori, T]]
-	[[Category: Montano, S.P]]
-	[[Category: Dementieva, I.S]]
	[[Category: Koide, S]]		[[Category: Koide, S]]
		+	[[Category: Montano, S P]]
		+	[[Category: Antibody]]
		+	[[Category: Fab]]
		+	[[Category: H3k9me3]]
		+	[[Category: Head-to-head dimerization]]
		+	[[Category: Immune system]]

OCA at 23:31, 15 October 2015

2015-10-15T23:31:05Z

←Older revision		Revision as of 23:31, 15 October 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Hattori, T., Dementieva, I.S., Montano, S.P., Koide, S.		Authors: Hattori, T., Dementieva, I.S., Montano, S.P., Koide, S.

OCA at 16:14, 5 August 2015

2015-08-05T16:14:36Z

←Older revision		Revision as of 16:14, 5 August 2015
Line 3:		Line 3:
	The entry 4yhp is ON HOLD		The entry 4yhp is ON HOLD

-	Authors: Hattori, T~~., Lai, D~~., Dementieva, I.S., Montano, S.P~~., Kurosawa, K., Zheng, Y., Akin, L.R., Swist-Rosowska, K.M., Grzybowski, A.T., Koide, A., Krajewski, K., Strahl, B.D., Kelleher, N.L., Ruthenburg, A.J~~., Koide, S.	+	Authors: Hattori, T., Dementieva, I.S., Montano, S.P., Koide, S.

	Description: Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide		Description: Crystal structure of 309M3-B Fab in complex with H3K9me3 peptide
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Hattori, T]]		[[Category: Hattori, T]]
-	[[Category: Ruthenburg, A.J]]
-	[[Category: Zheng, Y]]
-	[[Category: Krajewski, K]]
-	[[Category: Koide, A]]
-	[[Category: Strahl, B.D]]
-	[[Category: Akin, L.R]]
-	[[Category: Kurosawa, K]]
-	[[Category: Lai, D]]
	[[Category: Montano, S.P]]		[[Category: Montano, S.P]]
	[[Category: Dementieva, I.S]]		[[Category: Dementieva, I.S]]
-	[[Category: Grzybowski, A.T]]
	[[Category: Koide, S]]		[[Category: Koide, S]]
-	[[Category: Swist-Rosowska, K.M]]
-	[[Category: Kelleher, N.L]]

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

2015-03-11T10:37:51Z

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

←Older revision

Revision as of 10:37, 11 March 2015