1qbm - Revision history

OCA at 06:11, 3 April 2024

OCA — Wed, 03 Apr 2024 06:11:45 GMT

←Older revision		Revision as of 06:11, 3 April 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QBM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QBM FirstGlance]. <br>
-	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [https://pdbe.org/1qbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [https://www.ebi.ac.uk/pdbsum/1qbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qbm ProSAT]</span></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]] 2.37Å</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [https://pdbe.org/1qbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [https://www.ebi.ac.uk/pdbsum/1qbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qbm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KV5A3_MOUSE KV5A3_MOUSE]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 19:
	</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=1qbm 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=1qbm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A complete understanding of antibody-antigen association and specificity requires the stereochemical description of both antigen and antibody before and upon complex formation. The structural mechanism involved in the binding of the IgG1 monoclonal antibody E8 to its highly charged protein antigen horse cytochrome c (cyt c) is revealed by crystallographic structures of the antigen-binding fragment (Fab) of E8 bound to cyt c (FabE8-cytc), determined to 1.8 A resolution, and of uncomplexed Fab E8 (FabE8), determined to 2.26 A resolution. E8 antibody binds to three major discontiguous segments (33 to 39; 56 to 66; 96 to 104), and two minor sites on cyt c opposite to the exposed haem edge. Crystallographic definition of the E8 epitope complements and extends biochemical mapping and two-dimensional nuclear magnetic resonance with hydrogen-deuterium exchange studies. These combined results demonstrate that antibody-induced stabilization of secondary structural elements within the antigen can propagate locally to adjacent residues outside the epitope. Pre-existing shape complementarity at the FabE8-cytc interface is enhanced by 48 bound water molecules, and by local movements of up to 4.2 A for E8 antibody and 8.9 A for cyt c. Glu62, Asn103 and the C-terminal Glu104 of cyt c adjust to fit the pre-formed VL "hill" and VH "valley" shape of the grooved E8 paratope. All six E8 complementarity determining regions (CDRs) contact the antigen, with CDR L1 forming 46% of the total atomic contacts, and CDRs L1 (29%) and H3 (20%) contributing the highest percentage of the total surface area of E8 buried by cyt c (550 A2). The E8 antibody covers 534 A2 of the cyt c surface. The formation of five ion pairs between E8 and flexible cyt c residues Lys60, Glu62 and Glu104 suggests the importance of mobile regions and electrostatic interactions in providing the exquisite specificity needed for recognition of this extremely conserved protein antigen. The highly homologous VL domains of E8 and anti-lysozyme antibody D1. 3 achieve their distinct antigen-binding specificities by expanding the impact of their limited sequence differences through the recruitment of different sets of conserved residues and distinctly different CDR L3 conformations.
-
-	Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution.,Mylvaganam SE, Paterson Y, Getzoff ED J Mol Biol. 1998 Aug 14;281(2):301-22. PMID:9698550<ref>PMID:9698550</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1qbm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 30:		Line 24:
	*[[Sandbox 20009\|Sandbox 20009]]		*[[Sandbox 20009\|Sandbox 20009]]
	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]		*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Getzoff~~, E D~~]]	+	[[Category: Getzoff ED]]
-	[[Category: Mylvaganam~~, S E~~]]	+	[[Category: Mylvaganam SE]]
-	[[Category: Paterson, Y]]	+	[[Category: Paterson Y]]
-	~~[[Category: Anti-cytochrome c antibody]]~~	+
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Fab fragment]]~~	+
-	~~[[Category: Igg1 kappa]]~~	+
-	~~[[Category: Immunoglobulin~~]]	+

OCA at 09:40, 8 September 2021

OCA — Wed, 08 Sep 2021 09:40:27 GMT

←Older revision		Revision as of 09:40, 8 September 2021
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	<StructureSection load='1qbm' size='340' side='right'caption='[[1qbm]], [[Resolution\|resolution]] 2.37Å' scene=''>		<StructureSection load='1qbm' size='340' side='right'caption='[[1qbm]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QBM FirstGlance]. <br>
-	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [~~http~~://pdbe.org/1qbm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qbm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qbm ProSAT]</span></td></tr>	+	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [https://pdbe.org/1qbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [https://www.ebi.ac.uk/pdbsum/1qbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qbm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[Sandbox 20009\|Sandbox 20009]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:07, 27 November 2019

OCA — Wed, 27 Nov 2019 10:07:49 GMT

←Older revision		Revision as of 10:07, 27 November 2019
Line 1:		Line 1:

	==FAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION==		==FAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION==
-	<StructureSection load='1qbm' size='340' side='right' caption='[[1qbm]], [[Resolution\|resolution]] 2.37Å' scene=''>	+	<StructureSection load='1qbm' size='340' side='right'caption='[[1qbm]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBM FirstGlance]. <br>
Line 25:		Line 25:
	</div>		</div>
	<div class="pdbe-citations 1qbm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qbm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Getzoff, E D]]		[[Category: Getzoff, E D]]

OCA at 08:08, 24 February 2018

OCA — Sat, 24 Feb 2018 08:08:53 GMT

←Older revision		Revision as of 08:08, 24 February 2018
Line 1:		Line 1:
		+
	==FAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION==		==FAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION==
	<StructureSection load='1qbm' size='340' side='right' caption='[[1qbm]], [[Resolution\|resolution]] 2.37Å' scene=''>		<StructureSection load='1qbm' size='340' side='right' caption='[[1qbm]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBM FirstGlance]. <br>
-	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [http://pdbe.org/1qbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [http://www.ebi.ac.uk/pdbsum/1qbm PDBsum]</span></td></tr>	+	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [http://pdbe.org/1qbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [http://www.ebi.ac.uk/pdbsum/1qbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qbm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 9:		Line 10:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/1qbm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/1qbm_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=1qbm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 25:
	</div>		</div>
	<div class="pdbe-citations 1qbm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1qbm" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Antibody\|Antibody]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:59, 11 September 2015

OCA — Fri, 11 Sep 2015 12:59:41 GMT

←Older revision		Revision as of 12:59, 11 September 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBM FirstGlance]. <br>
-	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [http://www.ebi.ac.uk/pdbsum/1qbm PDBsum]</span></td></tr>	+	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [http://pdbe.org/1qbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [http://www.ebi.ac.uk/pdbsum/1qbm PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 23:		Line 23:
	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 1qbm" style="background-color:#fffaf0;"></div>

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

OCA at 08:02, 6 January 2015

OCA — Tue, 06 Jan 2015 08:02:37 GMT

←Older revision		Revision as of 08:02, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBM FirstGlance]. <br>
-	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [http://www.ebi.ac.uk/pdbsum/1qbm PDBsum]</span></td></tr>	+	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [http://www.ebi.ac.uk/pdbsum/1qbm 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 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Getzoff, E D.]]	+	[[Category: Getzoff, E D]]
-	[[Category: Mylvaganam, S E.]]	+	[[Category: Mylvaganam, S E]]
-	[[Category: Paterson, Y.]]	+	[[Category: Paterson, Y]]
	[[Category: Anti-cytochrome c antibody]]		[[Category: Anti-cytochrome c antibody]]
	[[Category: Antibody]]		[[Category: Antibody]]

OCA at 21:47, 28 September 2014

OCA — Sun, 28 Sep 2014 21:47:03 GMT

←Older revision		Revision as of 21:47, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1qbm.~~png\|left~~\|200px]]	+	==FAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION==
		+	<StructureSection load='1qbm' size='340' side='right' caption='[[1qbm]], [[Resolution\|resolution]] 2.37Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qbm]] 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=1QBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBM FirstGlance]. <br>
		+	</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=1qbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qbm RCSB], [http://www.ebi.ac.uk/pdbsum/1qbm 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/qb/1qbm_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 ==
		+	A complete understanding of antibody-antigen association and specificity requires the stereochemical description of both antigen and antibody before and upon complex formation. The structural mechanism involved in the binding of the IgG1 monoclonal antibody E8 to its highly charged protein antigen horse cytochrome c (cyt c) is revealed by crystallographic structures of the antigen-binding fragment (Fab) of E8 bound to cyt c (FabE8-cytc), determined to 1.8 A resolution, and of uncomplexed Fab E8 (FabE8), determined to 2.26 A resolution. E8 antibody binds to three major discontiguous segments (33 to 39; 56 to 66; 96 to 104), and two minor sites on cyt c opposite to the exposed haem edge. Crystallographic definition of the E8 epitope complements and extends biochemical mapping and two-dimensional nuclear magnetic resonance with hydrogen-deuterium exchange studies. These combined results demonstrate that antibody-induced stabilization of secondary structural elements within the antigen can propagate locally to adjacent residues outside the epitope. Pre-existing shape complementarity at the FabE8-cytc interface is enhanced by 48 bound water molecules, and by local movements of up to 4.2 A for E8 antibody and 8.9 A for cyt c. Glu62, Asn103 and the C-terminal Glu104 of cyt c adjust to fit the pre-formed VL "hill" and VH "valley" shape of the grooved E8 paratope. All six E8 complementarity determining regions (CDRs) contact the antigen, with CDR L1 forming 46% of the total atomic contacts, and CDRs L1 (29%) and H3 (20%) contributing the highest percentage of the total surface area of E8 buried by cyt c (550 A2). The E8 antibody covers 534 A2 of the cyt c surface. The formation of five ion pairs between E8 and flexible cyt c residues Lys60, Glu62 and Glu104 suggests the importance of mobile regions and electrostatic interactions in providing the exquisite specificity needed for recognition of this extremely conserved protein antigen. The highly homologous VL domains of E8 and anti-lysozyme antibody D1. 3 achieve their distinct antigen-binding specificities by expanding the impact of their limited sequence differences through the recruitment of different sets of conserved residues and distinctly different CDR L3 conformations.

-	~~{{STRUCTURE_1qbm\| PDB=1qbm \| SCENE= }}~~	+	Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution.,Mylvaganam SE, Paterson Y, Getzoff ED J Mol Biol. 1998 Aug 14;281(2):301-22. PMID:9698550<ref>PMID:9698550</ref>

-	~~===FAB E8B ANTIBODY~~, ~~X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9698550}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1qbm]] 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=1QBM OCA].~~	+

	==See Also==		==See Also==
	*[[Antibody\|Antibody]]		*[[Antibody\|Antibody]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009698550<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Getzoff, E D.]]		[[Category: Getzoff, E D.]]

OCA at 19:04, 20 October 2012

OCA — Sat, 20 Oct 2012 19:04:51 GMT

←Older revision		Revision as of 19:04, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1qbm]] is a 2 chain structure ~~of [[Antibody]]~~ 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=1QBM OCA].	+	[[1qbm]] 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=1QBM OCA].

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

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

OCA — Fri, 27 Jul 2012 06:13:18 GMT

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

←Older revision

Revision as of 06:13, 27 July 2012

OCA at 06:13, 27 July 2012

OCA — Fri, 27 Jul 2012 06:13:17 GMT

←Older revision		Revision as of 06:13, 27 July 2012
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-	{{Seed}}
	[[Image:1qbm.png\|left\|200px]]		[[Image:1qbm.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1qbm", 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),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1qbm\| PDB=1qbm \| SCENE= }}		{{STRUCTURE_1qbm\| PDB=1qbm \| SCENE= }}

	===FAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION===		===FAB E8B ANTIBODY, X-RAY STRUCTURE AT 2.37 ANGSTROMS RESOLUTION===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9698550}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9698550 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9698550}}		{{ABSTRACT_PUBMED_9698550}}

	==About this Structure==		==About this Structure==
-	~~1QBM~~ is a 2 ~~chains~~ structure of ~~sequences~~ 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=1QBM OCA].	+	[[1qbm]] is a 2 chain structure of [[Antibody]] 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=1QBM OCA].
		+
		+	==See Also==
		+	*[[Antibody\|Antibody]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9698550~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009698550</ref><references group="xtra"/>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Getzoff, E D.]]		[[Category: Getzoff, E D.]]
Line 33:		Line 24:
	[[Category: Igg1 kappa]]		[[Category: Igg1 kappa]]
	[[Category: Immunoglobulin]]		[[Category: Immunoglobulin]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 22:09:04 2009''