5cka - Revision history

OCA at 11:20, 10 January 2024

2024-01-10T11:20:41Z

←Older revision		Revision as of 11:20, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cka]] is a 1 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=5CKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CKA FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cka]] is a 1 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=5CKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CKA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5cka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cka OCA], [https://pdbe.org/5cka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cka RCSB], [https://www.ebi.ac.uk/pdbsum/5cka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cka 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=5cka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cka OCA], [https://pdbe.org/5cka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cka RCSB], [https://www.ebi.ac.uk/pdbsum/5cka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cka ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:11, 14 June 2023

2023-06-14T12:11:09Z

←Older revision		Revision as of 12:11, 14 June 2023
Line 3:		Line 3:
	<StructureSection load='5cka' size='340' side='right'caption='[[5cka]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5cka' size='340' side='right'caption='[[5cka]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cka]] is a 1 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=5CKA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cka]] is a 1 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=5CKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CKA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9t\|2z9t]], [[5cfh\|5cfh]]</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=5cka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cka OCA], [https://pdbe.org/5cka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cka RCSB], [https://www.ebi.ac.uk/pdbsum/5cka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cka ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B2M, CDABP0092, HDCMA22P ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5cka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cka OCA], [~~http~~://pdbe.org/5cka PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5cka RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5cka PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5cka ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Defects in B2M are the cause of hypercatabolic hypoproteinemia (HYCATHYP) [MIM:[~~http~~://omim.org/entry/241600 241600]]. Affected individuals show marked reduction in serum concentrations of immunoglobulin and albumin, probably due to rapid degradation.<ref>PMID:16549777</ref> Note=Beta-2-microglobulin may adopt the fibrillar configuration of amyloid in certain pathologic states. The capacity to assemble into amyloid fibrils is concentration dependent. Persistently high beta(2)-microglobulin serum levels lead to amyloidosis in patients on long-term hemodialysis.<ref>PMID:3532124</ref> <ref>PMID:1336137</ref> <ref>PMID:7554280</ref> <ref>PMID:4586824</ref> <ref>PMID:8084451</ref> <ref>PMID:12119416</ref> <ref>PMID:12796775</ref> <ref>PMID:16901902</ref> <ref>PMID:16491088</ref> <ref>PMID:17646174</ref> <ref>PMID:18835253</ref> <ref>PMID:18395224</ref> <ref>PMID:19284997</ref>	+	[https://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN] Defects in B2M are the cause of hypercatabolic hypoproteinemia (HYCATHYP) [MIM:[https://omim.org/entry/241600 241600]. Affected individuals show marked reduction in serum concentrations of immunoglobulin and albumin, probably due to rapid degradation.<ref>PMID:16549777</ref> Note=Beta-2-microglobulin may adopt the fibrillar configuration of amyloid in certain pathologic states. The capacity to assemble into amyloid fibrils is concentration dependent. Persistently high beta(2)-microglobulin serum levels lead to amyloidosis in patients on long-term hemodialysis.<ref>PMID:3532124</ref> <ref>PMID:1336137</ref> <ref>PMID:7554280</ref> <ref>PMID:4586824</ref> <ref>PMID:8084451</ref> <ref>PMID:12119416</ref> <ref>PMID:12796775</ref> <ref>PMID:16901902</ref> <ref>PMID:16491088</ref> <ref>PMID:17646174</ref> <ref>PMID:18835253</ref> <ref>PMID:18395224</ref> <ref>PMID:19284997</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system.	+	[https://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN] Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bolognesi, M]]	+	[[Category: Bolognesi M]]
-	[[Category: ~~Ricagno, S]]~~	+	[[Category: De Rosa M]]
-	~~[[Category:~~ Rosa, M De]]	+	[[Category: Ricagno S]]
-	[[Category: ~~Sala, B M~~]]	+	[[Category: Sala BM]]
-	[[Category: ~~Aggregation propensity]]~~	+
-	~~[[Category: Amyloid]]~~	+
-	~~[[Category: Beta-sandwitch]]~~	+
-	~~[[Category: Fold stability]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 11:42, 27 March 2020

2020-03-27T11:42:15Z

←Older revision		Revision as of 11:42, 27 March 2020
Line 1:		Line 1:

	==Human beta-2 microglobulin double mutant W60G-N83V==		==Human beta-2 microglobulin double mutant W60G-N83V==
-	<StructureSection load='5cka' size='340' side='right' caption='[[5cka]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5cka' size='340' side='right'caption='[[5cka]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cka]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cka]] is a 1 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=5CKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CKA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9t\|2z9t]], [[5cfh\|5cfh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9t\|2z9t]], [[5cfh\|5cfh]]</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=5cka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cka OCA], [http://pdbe.org/5cka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cka RCSB], [http://www.ebi.ac.uk/pdbsum/5cka PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">B2M, CDABP0092, HDCMA22P ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5cka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cka OCA], [http://pdbe.org/5cka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cka RCSB], [http://www.ebi.ac.uk/pdbsum/5cka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cka ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 5cka" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5cka" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bolognesi, M]]		[[Category: Bolognesi, M]]
	[[Category: Ricagno, S]]		[[Category: Ricagno, S]]

OCA at 15:50, 1 June 2016

2016-06-01T15:50:00Z

←Older revision		Revision as of 15:50, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5cka is ~~ON HOLD~~ ~~until Jul 15 2017~~	+	==Human beta-2 microglobulin double mutant W60G-N83V==
		+	<StructureSection load='5cka' size='340' side='right' caption='[[5cka]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5cka]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CKA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z9t\|2z9t]], [[5cfh\|5cfh]]</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=5cka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cka OCA], [http://pdbe.org/5cka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cka RCSB], [http://www.ebi.ac.uk/pdbsum/5cka PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Defects in B2M are the cause of hypercatabolic hypoproteinemia (HYCATHYP) [MIM:[http://omim.org/entry/241600 241600]]. Affected individuals show marked reduction in serum concentrations of immunoglobulin and albumin, probably due to rapid degradation.<ref>PMID:16549777</ref> Note=Beta-2-microglobulin may adopt the fibrillar configuration of amyloid in certain pathologic states. The capacity to assemble into amyloid fibrils is concentration dependent. Persistently high beta(2)-microglobulin serum levels lead to amyloidosis in patients on long-term hemodialysis.<ref>PMID:3532124</ref> <ref>PMID:1336137</ref> <ref>PMID:7554280</ref> <ref>PMID:4586824</ref> <ref>PMID:8084451</ref> <ref>PMID:12119416</ref> <ref>PMID:12796775</ref> <ref>PMID:16901902</ref> <ref>PMID:16491088</ref> <ref>PMID:17646174</ref> <ref>PMID:18835253</ref> <ref>PMID:18395224</ref> <ref>PMID:19284997</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/B2MG_HUMAN B2MG_HUMAN]] Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A wide range of human diseases is associated with mutations that, destabilizing proteins native state, promote their aggregation. However, the mechanisms leading from folded to aggregated states are still incompletely understood. To investigate these mechanisms, we used a combination of NMR spectroscopy and molecular dynamics simulations to compare the native state dynamics of Beta-2 microglobulin (beta2m), whose aggregation is associated with dialysis-related amyloidosis, and its aggregation-resistant mutant W60G. Our results indicate that W60G low aggregation propensity can be explained, beyond its higher stability, by an increased average protection of the aggregation-prone residues at its surface. To validate these findings, we designed beta2m variants that alter the aggregation-prone exposed surface of wild-type and W60G beta2m modifying their aggregation propensity. These results allowed us to pinpoint the role of dynamics in beta2m aggregation and to provide a new strategy to tune protein aggregation by modulating the exposure of aggregation-prone residues.

-	~~Authors:~~ Sala, ~~B.M.~~, De Rosa, M., Bolognesi, M., Ricagno, S.	+	Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability.,Camilloni C, Sala BM, Sormanni P, Porcari R, Corazza A, De Rosa M, Zanini S, Barbiroli A, Esposito G, Bolognesi M, Bellotti V, Vendruscolo M, Ricagno S Sci Rep. 2016 May 6;6:25559. doi: 10.1038/srep25559. PMID:27150430<ref>PMID:27150430</ref>

-	~~Description: Human beta~~-~~2 microglobulin double mutant W60G~~-~~N83V~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Ricagno, S]]~~	+	<div class="pdbe-citations 5cka" style="background-color:#fffaf0;"></div>
-	~~[[Category: De Rosa, M]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bolognesi, M]]		[[Category: Bolognesi, M]]
-	[[Category: Sala, B.M]]	+	[[Category: Ricagno, S]]
		+	[[Category: Rosa, M De]]
		+	[[Category: Sala, B M]]
		+	[[Category: Aggregation propensity]]
		+	[[Category: Amyloid]]
		+	[[Category: Beta-sandwitch]]
		+	[[Category: Fold stability]]
		+	[[Category: Immune system]]

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

2015-07-22T13:15:09Z

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

←Older revision

Revision as of 13:15, 22 July 2015

OCA: New page: '''Unreleased structure''' The entry 5cka is ON HOLD until Jul 15 2017 Authors: Sala, B.M., De Rosa, M., Bolognesi, M., Ricagno, S. Description: Human beta-2 microglobulin double mutan...

2015-07-22T13:15:08Z

New page: '''Unreleased structure''' The entry 5cka is ON HOLD until Jul 15 2017 Authors: Sala, B.M., De Rosa, M., Bolognesi, M., Ricagno, S. Description: Human beta-2 microglobulin double mutan...

New page

'''Unreleased structure'''

The entry 5cka is ON HOLD until Jul 15 2017

Authors: Sala, B.M., De Rosa, M., Bolognesi, M., Ricagno, S.

Description: Human beta-2 microglobulin double mutant W60G-N83V
[[Category: Unreleased Structures]]
[[Category: Ricagno, S]]
[[Category: De Rosa, M]]
[[Category: Bolognesi, M]]
[[Category: Sala, B.M]]