5jrp - Revision history

OCA at 19:03, 20 September 2023

2023-09-20T19:03:51Z

←Older revision		Revision as of 19:03, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jrp' size='340' side='right'caption='[[5jrp]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5jrp' size='340' side='right'caption='[[5jrp]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jrp]] is a 2 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=5JRP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JRP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jrp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JRP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JRP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2Å</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=5jrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrp OCA], [~~http~~://pdbe.org/5jrp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jrp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jrp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrp ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=5jrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrp OCA], [https://pdbe.org/5jrp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jrp RCSB], [https://www.ebi.ac.uk/pdbsum/5jrp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Crowe, J]]	+	[[Category: Crowe J]]
-	[[Category: Dong, J]]	+	[[Category: Dong J]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Marberg virus]]~~	+
-	~~[[Category: Monoclonal antibody~~]]	+

OCA at 11:35, 17 June 2020

2020-06-17T11:35:10Z

←Older revision		Revision as of 11:35, 17 June 2020
Line 1:		Line 1:

	==crystal structure of monoclonal antibody MR78 Fab==		==crystal structure of monoclonal antibody MR78 Fab==
-	<StructureSection load='5jrp' size='340' side='right' caption='[[5jrp]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5jrp' size='340' side='right'caption='[[5jrp]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jrp]] is a 2 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=5JRP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JRP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jrp]] is a 2 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=5JRP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JRP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=5jrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrp OCA], [http://pdbe.org/5jrp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrp RCSB], [http://www.ebi.ac.uk/pdbsum/5jrp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrp 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=5jrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrp OCA], [http://pdbe.org/5jrp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrp RCSB], [http://www.ebi.ac.uk/pdbsum/5jrp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Crowe, J]]		[[Category: Crowe, J]]
	[[Category: Dong, J]]		[[Category: Dong, J]]

OCA at 05:48, 25 April 2018

2018-04-25T05:48:31Z

←Older revision		Revision as of 05:48, 25 April 2018
Line 3:		Line 3:
	<StructureSection load='5jrp' size='340' side='right' caption='[[5jrp]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5jrp' size='340' side='right' caption='[[5jrp]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jrp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JRP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JRP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jrp]] is a 2 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=5JRP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JRP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=5jrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrp OCA], [http://pdbe.org/5jrp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrp RCSB], [http://www.ebi.ac.uk/pdbsum/5jrp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrp 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=5jrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrp OCA], [http://pdbe.org/5jrp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrp RCSB], [http://www.ebi.ac.uk/pdbsum/5jrp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrp ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	An atomic-detail model of the Marburg virus glycoprotein in complex with a neutralizing human monoclonal antibody designated MR78 was constructed using Phenix.Rosetta starting from a 3.6A crystallographic density map. The Asp at T6 in the HCDR3's bulged torso cannot form the canonical salt bridge as position T2 lacks an Arg or Lys residue. It instead engages in a hydrogen bond interaction with a Tyr contributed by the HCDR1 loop. This inter-CDR loop interaction stabilizes the bulged conformation needed for binding to the viral glycoprotein: a Tyr to Phe mutant displays a binding affinity reduced by a factor of at least 10. We found that 5% of a database of 465 million human antibody sequences has the same residues at T2 and T6 positions in HCDR3 and Tyr in HCDR1 that could potentially form this Asp-Tyr interaction, and that this interaction might contribute to a non-canonical bulged torso conformation.
		+
		+	Role of Non-local Interactions between CDR Loops in Binding Affinity of MR78 Antibody to Marburg Virus Glycoprotein.,Sangha AK, Dong J, Williamson L, Hashiguchi T, Saphire EO, Crowe JE Jr, Meiler J Structure. 2017 Dec 5;25(12):1820-1828.e2. doi: 10.1016/j.str.2017.10.005. Epub, 2017 Nov 16. PMID:29153506<ref>PMID:29153506</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jrp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Crowe, J]]		[[Category: Crowe, J]]
	[[Category: Dong, J]]		[[Category: Dong, J]]

OCA at 07:46, 8 November 2017

2017-11-08T07:46:36Z

←Older revision		Revision as of 07:46, 8 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jrp ~~is ON HOLD until Nov 08 2018~~	+	==crystal structure of monoclonal antibody MR78 Fab==
-		+	<StructureSection load='5jrp' size='340' side='right' caption='[[5jrp]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Dong, J~~.~~, Crowe, J~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jrp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JRP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JRP FirstGlance]. <br>
-	~~Description~~: ~~crystal structure of monoclonal antibody MR78 Fab~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5jrp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrp OCA], [http://pdbe.org/5jrp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrp RCSB], [http://www.ebi.ac.uk/pdbsum/5jrp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrp ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Crowe, J]]		[[Category: Crowe, J]]
	[[Category: Dong, J]]		[[Category: Dong, J]]
		+	[[Category: Immune system]]
		+	[[Category: Marberg virus]]
		+	[[Category: Monoclonal antibody]]

OCA at 10:46, 27 September 2017

2017-09-27T10:46:14Z

←Older revision		Revision as of 10:46, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jrp is ON HOLD until ~~Aug 09~~ 2018	+	The entry 5jrp is ON HOLD until Nov 08 2018

	Authors: Dong, J., Crowe, J.		Authors: Dong, J., Crowe, J.

OCA at 15:08, 15 March 2017

2017-03-15T15:08:52Z

←Older revision		Revision as of 15:08, 15 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jrp is ON HOLD until ~~Paper Publication~~	+	The entry 5jrp is ON HOLD until Aug 09 2018

	Authors: Dong, J., Crowe, J.		Authors: Dong, J., Crowe, J.

OCA at 10:00, 9 March 2017

2017-03-09T10:00:39Z

←Older revision		Revision as of 10:00, 9 March 2017
Line 7:		Line 7:
	Description: crystal structure of monoclonal antibody MR78 Fab		Description: crystal structure of monoclonal antibody MR78 Fab
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Dong, J]]
	[[Category: Crowe, J]]		[[Category: Crowe, J]]
		+	[[Category: Dong, J]]

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

2016-06-01T13:44:43Z

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

←Older revision

Revision as of 13:44, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jrp is ON HOLD until Paper Publication Authors: Dong, J., Crowe, J. Description: crystal structure of monoclonal antibody MR78 Fab [[Category: Unr...

2016-06-01T13:44:42Z

New page: '''Unreleased structure''' The entry 5jrp is ON HOLD until Paper Publication Authors: Dong, J., Crowe, J. Description: crystal structure of monoclonal antibody MR78 Fab [[Category: Unr...

New page

'''Unreleased structure'''

The entry 5jrp is ON HOLD until Paper Publication

Authors: Dong, J., Crowe, J.

Description: crystal structure of monoclonal antibody MR78 Fab
[[Category: Unreleased Structures]]
[[Category: Dong, J]]
[[Category: Crowe, J]]