7pkg - Revision history

OCA at 11:20, 23 October 2024

2024-10-23T11:20:05Z

← Older revision		Revision as of 11:20, 23 October 2024
Line 3:		Line 3:
	<StructureSection load='7pkg' size='340' side='right'caption='[[7pkg]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='7pkg' size='340' side='right'caption='[[7pkg]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[7pkg]] is a 5 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PKG FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PKG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.3Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=7pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pkg OCA], [https://pdbe.org/7pkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pkg RCSB], [https://www.ebi.ac.uk/pdbsum/7pkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pkg 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=7pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pkg OCA], [https://pdbe.org/7pkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pkg RCSB], [https://www.ebi.ac.uk/pdbsum/7pkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pkg ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[[https://www.uniprot.org/uniprot/CRP_HUMAN CRP_HUMAN]] Displays several functions associated with host defense: it promotes agglutination, bacterial capsular swelling, phagocytosis and complement fixation through its calcium-dependent binding to phosphorylcholine. Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells.
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The pentraxin family of proteins includes C-reactive protein (CRP), a canonical marker for the acute phase inflammatory response. As compared to normal physiological conditions in human serum, under conditions associated with damage and inflammation, such as acidosis and the oxidative burst, CRP exhibits modulated biochemical properties that may have a structural basis. Here, we explore how pH and ligand binding affect the structure and biochemical properties of CRP. Cryo-electron microscopy was used to solve structures of CRP at pH 7.5 or pH 5 and in the presence or absence of the ligand phosphocholine (PCh), which yielded 7 new high-resolution structures of CRP, including pentameric and decameric complexes. Structures previously derived from crystallography were imperfect pentagons, as shown by the variable angles between each subunit, whereas pentameric CRP derived from cryoEM was found to have C5 symmetry, with subunits forming a regular pentagon with equal angles. This discrepancy indicates flexibility at the interfaces of monomers that may relate to activation of the complement system by the C1 complex. CRP also appears to readily decamerise in solution into dimers of pentamers, which obscures the postulated binding sites for C1. Subtle structural rearrangements were observed between the conditions tested, including a putative change in histidine protonation that may prime the disulphide bridges for reduction and enhanced ability to activate the immune system. Enzyme-linked immunosorbent assays showed that CRP had markedly increased association to the C1 complex and immunoglobulins under conditions associated with acidosis, whilst a reduction in the Ca(2+) concentration lowered this pH-sensitivity for C1q, but not immunoglobulins, suggesting different modes of binding. These data suggest a model whereby a change in the ionic nature of CRP and immunological proteins can make it more adhesive to potential ligands without large structural rearrangements.

	Cryo-Electron Microscopy and Biochemical Analysis Offer Insights Into the Effects of Acidic pH, Such as Occur During Acidosis, on the Complement Binding Properties of C-Reactive Protein.,Noone DP, van der Velden TT, Sharp TH Front Immunol. 2021 Dec 16;12:757633. doi: 10.3389/fimmu.2021.757633. eCollection, 2021. PMID:34975846<ref>PMID:34975846</ref>		==See Also==
			*[[C-reactive protein\|C-reactive protein]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7pkg" style="background-color:#fffaf0;"></div>~~
	== ~~References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Noone~~, D P~~]]		[[Category: Noone DP]]
	[[Category: Sharp~~, T H]]~~		[[Category: Sharp TH]]
	~~[[Category: C-reactive protein]]~~
	~~[[Category: Crp]]~~
	~~[[Category: Immune system]]~~
	~~[[Category: Innate immunity~~]]

OCA at 10:04, 12 January 2022

2022-01-12T10:04:52Z

← Older revision		Revision as of 10:04, 12 January 2022
Line 1:		Line 1:

	==C-reactive protein pentamer at pH 5==		==C-reactive protein pentamer at pH 5==
	<StructureSection load='7pkg' size='340' side='right'caption='[[7pkg]]' scene=''>		<StructureSection load='7pkg' size='340' side='right'caption='[[7pkg]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PKG FirstGlance]. <br>		<table><tr><td colspan='2'>[[7pkg]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PKG 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=7pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pkg OCA], [https://pdbe.org/7pkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pkg RCSB], [https://www.ebi.ac.uk/pdbsum/7pkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pkg ProSAT]</span></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=7pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pkg OCA], [https://pdbe.org/7pkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pkg RCSB], [https://www.ebi.ac.uk/pdbsum/7pkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pkg ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/CRP_HUMAN CRP_HUMAN]] Displays several functions associated with host defense: it promotes agglutination, bacterial capsular swelling, phagocytosis and complement fixation through its calcium-dependent binding to phosphorylcholine. Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The pentraxin family of proteins includes C-reactive protein (CRP), a canonical marker for the acute phase inflammatory response. As compared to normal physiological conditions in human serum, under conditions associated with damage and inflammation, such as acidosis and the oxidative burst, CRP exhibits modulated biochemical properties that may have a structural basis. Here, we explore how pH and ligand binding affect the structure and biochemical properties of CRP. Cryo-electron microscopy was used to solve structures of CRP at pH 7.5 or pH 5 and in the presence or absence of the ligand phosphocholine (PCh), which yielded 7 new high-resolution structures of CRP, including pentameric and decameric complexes. Structures previously derived from crystallography were imperfect pentagons, as shown by the variable angles between each subunit, whereas pentameric CRP derived from cryoEM was found to have C5 symmetry, with subunits forming a regular pentagon with equal angles. This discrepancy indicates flexibility at the interfaces of monomers that may relate to activation of the complement system by the C1 complex. CRP also appears to readily decamerise in solution into dimers of pentamers, which obscures the postulated binding sites for C1. Subtle structural rearrangements were observed between the conditions tested, including a putative change in histidine protonation that may prime the disulphide bridges for reduction and enhanced ability to activate the immune system. Enzyme-linked immunosorbent assays showed that CRP had markedly increased association to the C1 complex and immunoglobulins under conditions associated with acidosis, whilst a reduction in the Ca(2+) concentration lowered this pH-sensitivity for C1q, but not immunoglobulins, suggesting different modes of binding. These data suggest a model whereby a change in the ionic nature of CRP and immunological proteins can make it more adhesive to potential ligands without large structural rearrangements.

			Cryo-Electron Microscopy and Biochemical Analysis Offer Insights Into the Effects of Acidic pH, Such as Occur During Acidosis, on the Complement Binding Properties of C-Reactive Protein.,Noone DP, van der Velden TT, Sharp TH Front Immunol. 2021 Dec 16;12:757633. doi: 10.3389/fimmu.2021.757633. eCollection, 2021. PMID:34975846<ref>PMID:34975846</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7pkg" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Noone DP]]		[[Category: Noone, D P]]
	[[Category: Sharp TH]]		[[Category: Sharp, T H]]
			[[Category: C-reactive protein]]
			[[Category: Crp]]
			[[Category: Immune system]]
			[[Category: Innate immunity]]

OCA at 15:27, 22 December 2021

2021-12-22T15:27:47Z

← Older revision		Revision as of 15:27, 22 December 2021
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7pkg is ~~ON HOLD until Paper Publication~~		==C-reactive protein pentamer at pH 5==
			<StructureSection load='7pkg' size='340' side='right'caption='[[7pkg]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PKG FirstGlance]. <br>
	~~Description~~:		</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=7pkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pkg OCA], [https://pdbe.org/7pkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pkg RCSB], [https://www.ebi.ac.uk/pdbsum/7pkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pkg ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Noone DP]]
			[[Category: Sharp TH]]

OCA: Protected "7pkg" [edit=sysop:move=sysop]

2021-09-08T07:34:58Z

Protected "7pkg" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:34, 8 September 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7pkg is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2021-09-08T07:34:57Z

New page: '''Unreleased structure''' The entry 7pkg is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7pkg is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]