4p4y - Revision history

OCA at 00:40, 28 December 2023

OCA — Thu, 28 Dec 2023 00:40:12 GMT

←Older revision		Revision as of 00:40, 28 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4p4y]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P4Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[4p4y]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P4Y FirstGlance]. <br>
-	</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=MAA:N-METHYL-L-ALANINE'>MAA</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.509Å</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=MAA:N-METHYL-L-ALANINE'>MAA</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4p4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p4y OCA], [https://pdbe.org/4p4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p4y RCSB], [https://www.ebi.ac.uk/pdbsum/4p4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p4y 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=4p4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p4y OCA], [https://pdbe.org/4p4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p4y RCSB], [https://www.ebi.ac.uk/pdbsum/4p4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p4y ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:42, 1 February 2023

OCA — Wed, 01 Feb 2023 12:42:06 GMT

←Older revision		Revision as of 12:42, 1 February 2023
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	<StructureSection load='4p4y' size='340' side='right'caption='[[4p4y]], [[Resolution\|resolution]] 1.51Å' scene=''>		<StructureSection load='4p4y' size='340' side='right'caption='[[4p4y]], [[Resolution\|resolution]] 1.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4p4y]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P4Y OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4P4Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4p4y]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P4Y 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=SO4:SULFATE+ION'>SO4</scene></td></tr>~~	+	</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=MAA:N-METHYL-L-ALANINE'>MAA</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MAA:N-METHYL-L-ALANINE'>MAA</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</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=4p4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p4y OCA], [https://pdbe.org/4p4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p4y RCSB], [https://www.ebi.ac.uk/pdbsum/4p4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p4y ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[4p4v\|4p4v]], [[4p4w\|4p4w]], [[4p4x\|4p4x]], [[4p4z\|4p4z]]~~</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=4p4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p4y OCA], [~~http~~://pdbe.org/4p4y PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4p4y RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4p4y PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4p4y ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Li, H~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Nowick, J S~~]]	+	[[Category: Li H]]
-	[[Category: ~~Spencer, R K~~]]	+	[[Category: Nowick JS]]
-	[[Category: ~~Amyloid]]~~	+	[[Category: Spencer RK]]
-	~~[[Category: Beta-2-microglobulin]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Hexamer]]~~	+
-	~~[[Category: Macrocycle~~]]	+

OCA at 17:47, 14 August 2019

OCA — Wed, 14 Aug 2019 17:47:12 GMT

←Older revision		Revision as of 17:47, 14 August 2019
Line 1:		Line 1:

	==Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK==		==Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK==
-	<StructureSection load='4p4y' size='340' side='right' caption='[[4p4y]], [[Resolution\|resolution]] 1.51Å' scene=''>	+	<StructureSection load='4p4y' size='340' side='right'caption='[[4p4y]], [[Resolution\|resolution]] 1.51Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4p4y]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P4Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[4p4y]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P4Y FirstGlance]. <br>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Li, H]]		[[Category: Li, H]]
	[[Category: Nowick, J S]]		[[Category: Nowick, J S]]

OCA at 17:25, 9 March 2017

OCA — Thu, 09 Mar 2017 17:25:54 GMT

←Older revision		Revision as of 17:25, 9 March 2017
Line 1:		Line 1:
		+
	==Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK==		==Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK==
	<StructureSection load='4p4y' size='340' side='right' caption='[[4p4y]], [[Resolution\|resolution]] 1.51Å' scene=''>		<StructureSection load='4p4y' size='340' side='right' caption='[[4p4y]], [[Resolution\|resolution]] 1.51Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAA:N-METHYL-L-ALANINE'>MAA</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAA:N-METHYL-L-ALANINE'>MAA</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p4v\|4p4v]], [[4p4w\|4p4w]], [[4p4x\|4p4x]], [[4p4z\|4p4z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p4v\|4p4v]], [[4p4w\|4p4w]], [[4p4x\|4p4x]], [[4p4z\|4p4z]]</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=4p4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4p4y RCSB], [http://www.ebi.ac.uk/pdbsum/4p4y 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=4p4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p4y OCA], [http://pdbe.org/4p4y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4p4y RCSB], [http://www.ebi.ac.uk/pdbsum/4p4y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4p4y ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4p4y" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:27, 13 May 2015

OCA — Wed, 13 May 2015 06:27:52 GMT

←Older revision		Revision as of 06:27, 13 May 2015
Line 8:		Line 8:
	<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=4p4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4p4y RCSB], [http://www.ebi.ac.uk/pdbsum/4p4y 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=4p4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4p4y RCSB], [http://www.ebi.ac.uk/pdbsum/4p4y PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Amyloid diseases such as Alzheimer's disease, Parkinson's disease, and type II diabetes share common features of toxic soluble protein oligomers. There are no structures at atomic resolution of oligomers formed by full-length amyloidogenic peptides and proteins, and only a few structures of oligomers formed by peptide fragments. The paucity of structural information provides a fundamental roadblock to understanding the pathology of amyloid diseases and developing preventions or therapies. Here, we present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of beta2-microglobulin (beta2m). Each macrocyclic peptide contains the heptapeptide sequence beta2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form beta-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of beta-sheets. These structures illustrate a common theme in which dimer and trimer subunits further associate to form a hydrophobic core. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers. A cocrystallization experiment in which a dodecamer-forming peptide recruits a hexamer-forming peptide to form mixed dodecamers demonstrates that one species can dictate the oligomerization of another. These findings should also be relevant to the formation of oligomers of full-length peptides and proteins in amyloid diseases.
		+
		+	X-ray Crystallographic Structures of Oligomers of Peptides Derived from beta-Microglobulin.,Spencer RK, Kreutzer AG, Salveson PJ, Li H, Nowick JS J Am Chem Soc. 2015 May 12. PMID:25915729<ref>PMID:25915729</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:56, 6 May 2015

OCA — Wed, 06 May 2015 12:56:12 GMT

←Older revision		Revision as of 12:56, 6 May 2015
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	==Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK==
-		+	<StructureSection load='4p4y' size='340' side='right' caption='[[4p4y]], [[Resolution\|resolution]] 1.51Å' scene=''>
-	~~The entry 4p4y is ON HOLD until Jun 17 2016~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4p4y]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P4Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P4Y FirstGlance]. <br>
-	~~Authors: Spencer, R.K., Li, H., Nowick, J.S.~~	+	</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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MAA:N-METHYL-L-ALANINE'>MAA</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=PHI:IODO-PHENYLALANINE'>PHI</scene></td></tr>
-	~~Description:~~ Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) -(ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p4v\|4p4v]], [[4p4w\|4p4w]], [[4p4x\|4p4x]], [[4p4z\|4p4z]]</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=4p4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p4y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4p4y RCSB], [http://www.ebi.ac.uk/pdbsum/4p4y PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Li, H]]		[[Category: Li, H]]
-	[[Category: Nowick, J.S]]	+	[[Category: Nowick, J S]]
-	[[Category: Spencer, R.K]]	+	[[Category: Spencer, R K]]
		+	[[Category: Amyloid]]
		+	[[Category: Beta-2-microglobulin]]
		+	[[Category: De novo protein]]
		+	[[Category: Hexamer]]
		+	[[Category: Macrocycle]]

OCA at 09:24, 25 February 2015

OCA — Wed, 25 Feb 2015 09:24:02 GMT

←Older revision		Revision as of 09:24, 25 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4p4y is ON HOLD until ~~Paper Publication~~	+	The entry 4p4y is ON HOLD until Jun 17 2016

	Authors: Spencer, R.K., Li, H., Nowick, J.S.		Authors: Spencer, R.K., Li, H., Nowick, J.S.

OCA at 14:46, 24 December 2014

OCA — Wed, 24 Dec 2014 14:46:55 GMT

←Older revision		Revision as of 14:46, 24 December 2014
Line 6:		Line 6:

	Description: Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) -(ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK		Description: Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) -(ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK
		+	[[Category: Unreleased Structures]]
		+	[[Category: Li, H]]
		+	[[Category: Nowick, J.S]]
		+	[[Category: Spencer, R.K]]

OCA at 06:33, 27 August 2014

OCA — Wed, 27 Aug 2014 06:33:35 GMT

←Older revision		Revision as of 06:33, 27 August 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4p4y is ON HOLD	+	The entry 4p4y is ON HOLD until Paper Publication

	Authors: Spencer, R.K., Li, H., Nowick, J.S.		Authors: Spencer, R.K., Li, H., Nowick, J.S.

	Description: Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) -(ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK		Description: Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) -(ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK

OCA at 05:52, 9 April 2014

OCA — Wed, 09 Apr 2014 05:52:15 GMT

←Older revision		Revision as of 05:52, 9 April 2014
Line 3:		Line 3:
	The entry 4p4y is ON HOLD		The entry 4p4y is ON HOLD

-	Authors: Spencer, R.K., ~~Hao~~, L., Nowick, J.S.	+	Authors: Spencer, R.K., Li, H., Nowick, J.S.

	Description: Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) -(ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK		Description: Hexamer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) -(ORN)YLL(PHI)YTE(ORN)KVT(MAA)TVK