4nja - Revision history

OCA at 16:58, 20 September 2023

OCA — Wed, 20 Sep 2023 16:58:07 GMT

←Older revision		Revision as of 16:58, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nja]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NJA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nja]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NJA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2M9:8-METHOXYPYRENE-1,3,6-TRISULFONIC+ACID'>2M9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.204Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2M9:8-METHOXYPYRENE-1,3,6-TRISULFONIC+ACID'>2M9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4nja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nja OCA], [https://pdbe.org/4nja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nja RCSB], [https://www.ebi.ac.uk/pdbsum/4nja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nja 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=4nja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nja OCA], [https://pdbe.org/4nja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nja RCSB], [https://www.ebi.ac.uk/pdbsum/4nja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nja ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:30, 11 January 2023

OCA — Wed, 11 Jan 2023 08:30:46 GMT

←Older revision		Revision as of 08:30, 11 January 2023
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	<StructureSection load='4nja' size='340' side='right'caption='[[4nja]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4nja' size='340' side='right'caption='[[4nja]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nja]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NJA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NJA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nja]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NJA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2M9:8-METHOXYPYRENE-1,3,6-TRISULFONIC+ACID'>2M9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2M9:8-METHOXYPYRENE-1,3,6-TRISULFONIC+ACID'>2M9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nj9\|4nj9]]~~</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=4nja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nja OCA], [https://pdbe.org/4nja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nja RCSB], [https://www.ebi.ac.uk/pdbsum/4nja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nja 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=4nja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nja OCA], [~~http~~://pdbe.org/4nja PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nja RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nja PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nja ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KV3A8_MOUSE KV3A8_MOUSE] [https://www.uniprot.org/uniprot/Q52L95_MOUSE Q52L95_MOUSE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Romesberg~~, F E~~]]	+	[[Category: Romesberg FE]]
-	[[Category: Stanfield~~, R L~~]]	+	[[Category: Stanfield RL]]
-	[[Category: Wilson~~, I A~~]]	+	[[Category: Wilson IA]]
-	[[Category: Zimmermann, J]]	+	[[Category: Zimmermann J]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Immunoglobulin fold]]~~	+
-	~~[[Category: Mpts binding~~]]	+

OCA at 04:56, 13 February 2020

OCA — Thu, 13 Feb 2020 04:56:16 GMT

←Older revision		Revision as of 04:56, 13 February 2020
Line 1:		Line 1:

	==Crystal structure of Fab 6C8 in complex with MPTS==		==Crystal structure of Fab 6C8 in complex with MPTS==
-	<StructureSection load='4nja' size='340' side='right' caption='[[4nja]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4nja' size='340' side='right'caption='[[4nja]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nja]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NJA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NJA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nja]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NJA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NJA FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Romesberg, F E]]		[[Category: Romesberg, F E]]

OCA at 17:16, 18 January 2017

OCA — Wed, 18 Jan 2017 17:16:39 GMT

←Older revision		Revision as of 17:16, 18 January 2017
Line 1:		Line 1:
		+
	==Crystal structure of Fab 6C8 in complex with MPTS==		==Crystal structure of Fab 6C8 in complex with MPTS==
	<StructureSection load='4nja' size='340' side='right' caption='[[4nja]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4nja' size='340' side='right' caption='[[4nja]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2M9:8-METHOXYPYRENE-1,3,6-TRISULFONIC+ACID'>2M9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2M9:8-METHOXYPYRENE-1,3,6-TRISULFONIC+ACID'>2M9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nj9\|4nj9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nj9\|4nj9]]</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=4nja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nja OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nja RCSB], [http://www.ebi.ac.uk/pdbsum/4nja 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=4nja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nja OCA], [http://pdbe.org/4nja PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nja RCSB], [http://www.ebi.ac.uk/pdbsum/4nja PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nja ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4nja" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:17, 26 March 2015

OCA — Thu, 26 Mar 2015 07:17:21 GMT

←Older revision		Revision as of 07:17, 26 March 2015
Line 7:		Line 7:
	<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=4nja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nja OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nja RCSB], [http://www.ebi.ac.uk/pdbsum/4nja 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=4nja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nja OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nja RCSB], [http://www.ebi.ac.uk/pdbsum/4nja PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.
		+
		+	Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation.,Adhikary R, Yu W, Oda M, Walker RC, Chen T, Stanfield RL, Wilson IA, Zimmermann J, Romesberg FE Biochemistry. 2015 Mar 24;54(11):2085-93. doi: 10.1021/bi501417q. Epub 2015 Mar, 10. PMID:25756188<ref>PMID:25756188</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:52, 12 November 2014

OCA — Wed, 12 Nov 2014 06:52:13 GMT

←Older revision		Revision as of 06:52, 12 November 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of Fab 6C8 in complex with MPTS==
-		+	<StructureSection load='4nja' size='340' side='right' caption='[[4nja]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~The entry~~ 4nja is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4nja]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NJA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NJA FirstGlance]. <br>
-	~~Authors~~: ~~Stanfield~~, R.L., ~~Romesberg, F~~.E., ~~Zimmermann, J~~., Wilson, I.A.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2M9:8-METHOXYPYRENE-1,3,6-TRISULFONIC+ACID'>2M9</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nj9\|4nj9]]</td></tr>
-	~~Description~~: ~~Crystal structure of Fab 6C8 in complex with MPTS~~	+	<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=4nja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nja OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nja RCSB], [http://www.ebi.ac.uk/pdbsum/4nja PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Mus musculus]]
		+	[[Category: Romesberg, F E]]
		+	[[Category: Stanfield, R L]]
		+	[[Category: Wilson, I A]]
		+	[[Category: Zimmermann, J]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin fold]]
		+	[[Category: Mpts binding]]

OCA at 09:13, 8 January 2014

OCA — Wed, 08 Jan 2014 09:13:44 GMT

←Older revision		Revision as of 09:13, 8 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Stanfield, R.L., Romesberg, F.E., Zimmermann, J., Wilson, I.A.		Authors: Stanfield, R.L., Romesberg, F.E., Zimmermann, J., Wilson, I.A.

	Description: Crystal structure of Fab 6C8 in complex with MPTS		Description: Crystal structure of Fab 6C8 in complex with MPTS

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

OCA — Wed, 20 Nov 2013 12:59:19 GMT

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

←Older revision

Revision as of 12:59, 20 November 2013

OCA: New page: '''Unreleased structure''' The entry 4nja is ON HOLD Authors: Stanfield, R.L., Romesberg, F.E., Zimmermann, J., Wilson, I.A. Description: Crystal structure of Fab 6C8 in complex with M...

OCA — Wed, 20 Nov 2013 12:59:17 GMT

New page: '''Unreleased structure''' The entry 4nja is ON HOLD Authors: Stanfield, R.L., Romesberg, F.E., Zimmermann, J., Wilson, I.A. Description: Crystal structure of Fab 6C8 in complex with M...

New page

'''Unreleased structure'''

The entry 4nja is ON HOLD

Authors: Stanfield, R.L., Romesberg, F.E., Zimmermann, J., Wilson, I.A.

Description: Crystal structure of Fab 6C8 in complex with MPTS