5i5k - Revision history

OCA at 08:23, 23 August 2023

OCA — Wed, 23 Aug 2023 08:23:55 GMT

←Older revision		Revision as of 08:23, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='5i5k' size='340' side='right'caption='[[5i5k]], [[Resolution\|resolution]] 4.20Å' scene=''>		<StructureSection load='5i5k' size='340' side='right'caption='[[5i5k]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i5k]] is a 6 chain structure with sequence from [~~http://en.wikipedia.org/wiki/Human Human] and [http~~://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I5K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5I5K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i5k]] is a 6 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=5I5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I5K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 4.2Å</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=5i5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i5k OCA], [~~http~~://pdbe.org/5i5k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i5k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i5k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i5k ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5i5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i5k OCA], [https://pdbe.org/5i5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i5k RCSB], [https://www.ebi.ac.uk/pdbsum/5i5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i5k ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/CO5_HUMAN CO5_HUMAN]] Defects in C5 are the cause of complement component 5 deficiency (C5D) [MIM:[~~http~~://omim.org/entry/609536 609536]]. A rare defect of the complement classical pathway associated with susceptibility to severe recurrent infections, predominantly by Neisseria gonorrhoeae or Neisseria meningitidis. Note=An association study of C5 haplotypes and genotypes in individuals with chronic hepatitis C virus infection shows that individuals homozygous for the C5_1 haplotype have a significantly higher stage of liver fibrosis than individuals carrying at least 1 other allele (PubMed:15995705).	+	[https://www.uniprot.org/uniprot/CO5_HUMAN CO5_HUMAN] Defects in C5 are the cause of complement component 5 deficiency (C5D) [MIM:[https://omim.org/entry/609536 609536]. A rare defect of the complement classical pathway associated with susceptibility to severe recurrent infections, predominantly by Neisseria gonorrhoeae or Neisseria meningitidis. Note=An association study of C5 haplotypes and genotypes in individuals with chronic hepatitis C virus infection shows that individuals homozygous for the C5_1 haplotype have a significantly higher stage of liver fibrosis than individuals carrying at least 1 other allele (PubMed:15995705).
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CO5_HUMAN CO5_HUMAN]] Activation of C5 by a C5 convertase initiates the spontaneous assembly of the late complement components, C5-C9, into the membrane attack complex. C5b has a transient binding site for C6. The C5b-C6 complex is the foundation upon which the lytic complex is assembled. Derived from proteolytic degradation of complement C5, C5 anaphylatoxin is a mediator of local inflammatory process. It induces the contraction of smooth muscle, increases vascular permeability and causes histamine release from mast cells and basophilic leukocytes. C5a also stimulates the locomotion of polymorphonuclear leukocytes (chemokinesis) and direct their migration toward sites of inflammation (chemotaxis).	+	[https://www.uniprot.org/uniprot/CO5_HUMAN CO5_HUMAN] Activation of C5 by a C5 convertase initiates the spontaneous assembly of the late complement components, C5-C9, into the membrane attack complex. C5b has a transient binding site for C6. The C5b-C6 complex is the foundation upon which the lytic complex is assembled. Derived from proteolytic degradation of complement C5, C5 anaphylatoxin is a mediator of local inflammatory process. It induces the contraction of smooth muscle, increases vascular permeability and causes histamine release from mast cells and basophilic leukocytes. C5a also stimulates the locomotion of polymorphonuclear leukocytes (chemokinesis) and direct their migration toward sites of inflammation (chemotaxis).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 24:
	==See Also==		==See Also==
	*[[Complement C5 3D structures\|Complement C5 3D structures]]		*[[Complement C5 3D structures\|Complement C5 3D structures]]
		+	*[[Monoclonal Antibodies 3D structures\|Monoclonal Antibodies 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Andersen~~, G R~~]]	+	[[Category: Andersen GR]]
-	[[Category: Schatz-Jakobsen~~, J A]]~~	+	[[Category: Schatz-Jakobsen JA]]
-	~~[[Category: Complement]]~~	+
-	~~[[Category: Fab]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 07:05, 3 June 2020

OCA — Wed, 03 Jun 2020 07:05:31 GMT

←Older revision		Revision as of 07:05, 3 June 2020
Line 1:		Line 1:

	==Structure of complement C5 in complex with eculizumab==		==Structure of complement C5 in complex with eculizumab==
-	<StructureSection load='5i5k' size='340' side='right' caption='[[5i5k]], [[Resolution\|resolution]] 4.20Å' scene=''>	+	<StructureSection load='5i5k' size='340' side='right'caption='[[5i5k]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i5k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I5K OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I5K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i5k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I5K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5I5K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5i5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i5k OCA], [http://pdbe.org/5i5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i5k RCSB], [http://www.ebi.ac.uk/pdbsum/5i5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i5k 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=5i5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i5k OCA], [http://pdbe.org/5i5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i5k RCSB], [http://www.ebi.ac.uk/pdbsum/5i5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i5k ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5i5k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5i5k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Complement C5 3D structures\|Complement C5 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Andersen, G R]]		[[Category: Andersen, G R]]
	[[Category: Schatz-Jakobsen, J A]]		[[Category: Schatz-Jakobsen, J A]]

OCA at 18:01, 12 July 2016

OCA — Tue, 12 Jul 2016 18:01:34 GMT

←Older revision		Revision as of 18:01, 12 July 2016
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5i5k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I5K FirstGlance]. <br>		<table><tr><td colspan='2'>[[5i5k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I5K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5i5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i5k OCA], [http://pdbe.org/5i5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i5k RCSB], [http://www.ebi.ac.uk/pdbsum/5i5k 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=5i5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i5k OCA], [http://pdbe.org/5i5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i5k RCSB], [http://www.ebi.ac.uk/pdbsum/5i5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i5k ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 07:50, 20 June 2016

OCA — Mon, 20 Jun 2016 07:50:55 GMT

←Older revision		Revision as of 07:50, 20 June 2016
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CO5_HUMAN CO5_HUMAN]] Activation of C5 by a C5 convertase initiates the spontaneous assembly of the late complement components, C5-C9, into the membrane attack complex. C5b has a transient binding site for C6. The C5b-C6 complex is the foundation upon which the lytic complex is assembled. Derived from proteolytic degradation of complement C5, C5 anaphylatoxin is a mediator of local inflammatory process. It induces the contraction of smooth muscle, increases vascular permeability and causes histamine release from mast cells and basophilic leukocytes. C5a also stimulates the locomotion of polymorphonuclear leukocytes (chemokinesis) and direct their migration toward sites of inflammation (chemotaxis).		[[http://www.uniprot.org/uniprot/CO5_HUMAN CO5_HUMAN]] Activation of C5 by a C5 convertase initiates the spontaneous assembly of the late complement components, C5-C9, into the membrane attack complex. C5b has a transient binding site for C6. The C5b-C6 complex is the foundation upon which the lytic complex is assembled. Derived from proteolytic degradation of complement C5, C5 anaphylatoxin is a mediator of local inflammatory process. It induces the contraction of smooth muscle, increases vascular permeability and causes histamine release from mast cells and basophilic leukocytes. C5a also stimulates the locomotion of polymorphonuclear leukocytes (chemokinesis) and direct their migration toward sites of inflammation (chemotaxis).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Eculizumab is a humanized mAb approved for treatment of patients with paroxysmal nocturnal hemoglobinuria and atypical hemolytic uremic syndrome. Eculizumab binds complement component C5 and prevents its cleavage by C5 convertases, inhibiting release of both the proinflammatory metabolite C5a and formation of the membrane attack complex via C5b. In this study, we present the crystal structure of the complex between C5 and a Fab fragment with the same sequence as eculizumab at a resolution of 4.2 A. Five CDRs contact the C5 macroglobulin 7 domain, which contains the entire epitope. A complete mutational scan of the 66 CDR residues identified 28 residues as important for the C5-eculizumab interaction, and the structure of the complex offered an explanation for the reduced C5 binding observed for these mutant Abs. Furthermore, the structural observations of the interaction are supported by the reduced ability of a subset of these mutated Abs to inhibit membrane attack complex formation as tested in a hemolysis assay. Our results suggest that eculizumab functions by sterically preventing C5 from binding to convertases and explain the exquisite selectivity of eculizumab for human C5 and how polymorphisms in C5 cause eculizumab-resistance in a small number of patients with paroxysmal nocturnal hemoglobinuria.
		+
		+	Structural Basis for Eculizumab-Mediated Inhibition of the Complement Terminal Pathway.,Schatz-Jakobsen JA, Zhang Y, Johnson K, Neill A, Sheridan D, Andersen GR J Immunol. 2016 Jul 1;197(1):337-44. doi: 10.4049/jimmunol.1600280. Epub 2016 May, 18. PMID:27194791<ref>PMID:27194791</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5i5k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 03:53, 11 May 2016

OCA — Wed, 11 May 2016 03:53:03 GMT

←Older revision		Revision as of 03:53, 11 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5i5k is ~~ON HOLD~~	+	==Structure of complement C5 in complex with eculizumab==
-		+	<StructureSection load='5i5k' size='340' side='right' caption='[[5i5k]], [[Resolution\|resolution]] 4.20Å' scene=''>
-	~~Authors~~: ~~Schatz~~-~~Jakobsen~~, J. A, ~~Andersen~~, G.R.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5i5k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I5K FirstGlance]. <br>
-	~~Description~~: ~~Complement factor~~ in ~~complex~~ with ~~Fab fragment~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5i5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i5k OCA], [http://pdbe.org/5i5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i5k RCSB], [http://www.ebi.ac.uk/pdbsum/5i5k PDBsum]</span></td></tr>
-	[[Category: Schatz-Jakobsen, J. A~~, Andersen, G.R~~]]	+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/CO5_HUMAN CO5_HUMAN]] Defects in C5 are the cause of complement component 5 deficiency (C5D) [MIM:[http://omim.org/entry/609536 609536]]. A rare defect of the complement classical pathway associated with susceptibility to severe recurrent infections, predominantly by Neisseria gonorrhoeae or Neisseria meningitidis. Note=An association study of C5 haplotypes and genotypes in individuals with chronic hepatitis C virus infection shows that individuals homozygous for the C5_1 haplotype have a significantly higher stage of liver fibrosis than individuals carrying at least 1 other allele (PubMed:15995705).
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CO5_HUMAN CO5_HUMAN]] Activation of C5 by a C5 convertase initiates the spontaneous assembly of the late complement components, C5-C9, into the membrane attack complex. C5b has a transient binding site for C6. The C5b-C6 complex is the foundation upon which the lytic complex is assembled. Derived from proteolytic degradation of complement C5, C5 anaphylatoxin is a mediator of local inflammatory process. It induces the contraction of smooth muscle, increases vascular permeability and causes histamine release from mast cells and basophilic leukocytes. C5a also stimulates the locomotion of polymorphonuclear leukocytes (chemokinesis) and direct their migration toward sites of inflammation (chemotaxis).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Andersen, G R]]
		+	[[Category: Schatz-Jakobsen, J A]]
		+	[[Category: Complement]]
		+	[[Category: Fab]]
		+	[[Category: Immune system]]

OCA at 13:24, 2 March 2016

OCA — Wed, 02 Mar 2016 13:24:33 GMT

←Older revision		Revision as of 13:24, 2 March 2016
Line 3:		Line 3:
	The entry 5i5k is ON HOLD		The entry 5i5k is ON HOLD

-	Authors: Schatz-Jakobsen, J.A., Andersen, G.R.	+	Authors: Schatz-Jakobsen, J. A, Andersen, G.R.

	Description: Complement factor in complex with Fab fragment		Description: Complement factor in complex with Fab fragment
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Schatz-Jakobsen, J.A]]	+	[[Category: Schatz-Jakobsen, J. A, Andersen, G.R]]
-	~~[[Category:~~ Andersen, G.R]]	+

OCA: Protected "5i5k" [edit=sysop:move=sysop]

OCA — Fri, 26 Feb 2016 16:48:55 GMT

Protected "5i5k" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:48, 26 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i5k is ON HOLD Authors: Schatz-Jakobsen, J.A., Andersen, G.R. Description: Complement factor in complex with Fab fragment [[Category: Unreleased S...

OCA — Fri, 26 Feb 2016 16:48:53 GMT

New page: '''Unreleased structure''' The entry 5i5k is ON HOLD Authors: Schatz-Jakobsen, J.A., Andersen, G.R. Description: Complement factor in complex with Fab fragment [[Category: Unreleased S...

New page

'''Unreleased structure'''

The entry 5i5k is ON HOLD

Authors: Schatz-Jakobsen, J.A., Andersen, G.R.

Description: Complement factor in complex with Fab fragment
[[Category: Unreleased Structures]]
[[Category: Schatz-Jakobsen, J.A]]
[[Category: Andersen, G.R]]