6tdq - Revision history

OCA at 13:00, 24 January 2024

OCA — Wed, 24 Jan 2024 13:00:26 GMT

←Older revision		Revision as of 13:00, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6tdq' size='340' side='right'caption='[[6tdq]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6tdq' size='340' side='right'caption='[[6tdq]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tdq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TDQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6TDQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tdq]] is a 4 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=6TDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TDQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</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]] 1.6Å</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=6tdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tdq OCA], [~~http~~://pdbe.org/6tdq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tdq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tdq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tdq ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</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=6tdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tdq OCA], [https://pdbe.org/6tdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tdq RCSB], [https://www.ebi.ac.uk/pdbsum/6tdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tdq ProSAT]</span></td></tr>
	</table>		</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 ==		== 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/F6IQS1_HUMAN F6IQS1_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6tdq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6tdq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-2 microglobulin 3D structures\|Beta-2 microglobulin 3D structures]]
		+	*[[MHC 3D structures\|MHC 3D structures]]
		+	*[[MHC I 3D structures\|MHC I 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Alai, M Garcia~~]]	+	[[Category: Anjanappa R]]
-	[[Category: ~~Anjanappa, R~~]]	+	[[Category: Garcia Alai M]]
-	[[Category: Meijers, R]]	+	[[Category: Meijers R]]
-	[[Category: Springer, S]]	+	[[Category: Springer S]]
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Mhc class i molecule~~]]	+

OCA at 10:19, 27 March 2020

OCA — Fri, 27 Mar 2020 10:19:20 GMT

←Older revision		Revision as of 10:19, 27 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6tdq is ~~ON HOLD~~	+	==Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM dipeptide in the A pocket and one GM dipeptide in the F pocket.==
		+	<StructureSection load='6tdq' size='340' side='right'caption='[[6tdq]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6tdq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TDQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TDQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</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=6tdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tdq OCA], [http://pdbe.org/6tdq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tdq RCSB], [http://www.ebi.ac.uk/pdbsum/6tdq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tdq ProSAT]</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 ==
		+	Major Histocompatibility Complex (MHC) class I molecules selectively bind peptides for presentation to cytotoxic T cells. The peptide-free state of these molecules is not well understood. Here, we characterize a disulfide-stabilized version of the human class I molecule HLA-A02:01 that is stable in the absence of peptide and can readily exchange cognate peptides. We present X-ray crystal structures of the peptide-free state of HLA-A02:01, together with structures that have dipeptides bound in the A and F pockets. These structural snapshots reveal that the amino acid side chains lining the binding pockets switch in a coordinated fashion between a peptide-free unlocked state and a peptide-bound locked state. Molecular dynamics simulations suggest that the opening and closing of the F pocket affects peptide ligand conformations in adjacent binding pockets. We propose that peptide binding is co-determined by synergy between the binding pockets of the MHC molecule.

-	~~Authors: Anjanappa~~, R., Garcia Alai, M., ~~Springer~~, S., Meijers, R.	+	Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection.,Anjanappa R, Garcia-Alai M, Kopicki JD, Lockhauserbaumer J, Aboelmagd M, Hinrichs J, Nemtanu IM, Uetrecht C, Zacharias M, Springer S, Meijers R Nat Commun. 2020 Mar 11;11(1):1314. doi: 10.1038/s41467-020-14862-4. PMID:32161266<ref>PMID:32161266</ref>

-	~~Description: Crystal structure~~ of the ~~disulfide engineered HLA-A0201 molecule in complex with one GM dipeptide in the A pocket and one GM dipeptide in the F pocket~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Springer, S]]~~	+	<div class="pdbe-citations 6tdq" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Meijers, R~~]]	+	== References ==
-	[[Category: ~~Garcia~~ Alai, M]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Alai, M Garcia]]
	[[Category: Anjanappa, R]]		[[Category: Anjanappa, R]]
		+	[[Category: Meijers, R]]
		+	[[Category: Springer, S]]
		+	[[Category: Immune system]]
		+	[[Category: Mhc class i molecule]]

OCA: Protected "6tdq" [edit=sysop:move=sysop]

OCA — Wed, 20 Nov 2019 13:38:03 GMT

Protected "6tdq" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:38, 20 November 2019

OCA: New page: '''Unreleased structure''' The entry 6tdq is ON HOLD Authors: Anjanappa, R., Garcia Alai, M., Springer, S., Meijers, R. Description: Crystal structure of the disulfide engineered HLA-A...

OCA — Wed, 20 Nov 2019 13:38:01 GMT

New page: '''Unreleased structure''' The entry 6tdq is ON HOLD Authors: Anjanappa, R., Garcia Alai, M., Springer, S., Meijers, R. Description: Crystal structure of the disulfide engineered HLA-A...

New page

'''Unreleased structure'''

The entry 6tdq is ON HOLD

Authors: Anjanappa, R., Garcia Alai, M., Springer, S., Meijers, R.

Description: Crystal structure of the disulfide engineered HLA-A0201 molecule in complex with one GM dipeptide in the A pocket and one GM dipeptide in the F pocket.
[[Category: Unreleased Structures]]
[[Category: Springer, S]]
[[Category: Meijers, R]]
[[Category: Garcia Alai, M]]
[[Category: Anjanappa, R]]