OCA at 12:31, 24 January 2024

OCA — Wed, 24 Jan 2024 12:31:04 GMT

←Older revision		Revision as of 12:31, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6ryf' size='340' side='right'caption='[[6ryf]], [[Resolution\|resolution]] 1.72Å' scene=''>		<StructureSection load='6ryf' size='340' side='right'caption='[[6ryf]], [[Resolution\|resolution]] 1.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ryf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RYF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ryf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RYF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.72Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KF2:'>KF2</scene></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=KF2:[(1~{R})-1-azanyl-3-phenyl-propyl]-[(2~{S})-2-methanoyl-4-methyl-pentyl]phosphinic+acid'>KF2</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rqx\|6rqx]]~~</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=6ryf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ryf OCA], [https://pdbe.org/6ryf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ryf RCSB], [https://www.ebi.ac.uk/pdbsum/6ryf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ryf ProSAT]</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=6ryf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ryf OCA], [~~http~~://pdbe.org/6ryf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ryf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ryf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ryf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ERAP1_HUMAN ERAP1_HUMAN]] Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I-binding peptides. Peptide trimming is essential to customize longer precursor peptides to fit them to the correct length required for presentation on MHC class I molecules. Strongly prefers substrates 9-16 residues long. Rapidly degrades 13-mer to a 9-mer and then stops. Preferentially hydrolyzes the residue Leu and peptides with a hydrophobic C-terminus, while it has weak activity toward peptides with charged C-terminus. May play a role in the inactivation of peptide hormones. May be involved in the regulation of blood pressure through the inactivation of angiotensin II and/or the generation of bradykinin in the kidney.<ref>PMID:15908954</ref> <ref>PMID:16286653</ref> <ref>PMID:21478864</ref>	+	[https://www.uniprot.org/uniprot/ERAP1_HUMAN ERAP1_HUMAN] Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I-binding peptides. Peptide trimming is essential to customize longer precursor peptides to fit them to the correct length required for presentation on MHC class I molecules. Strongly prefers substrates 9-16 residues long. Rapidly degrades 13-mer to a 9-mer and then stops. Preferentially hydrolyzes the residue Leu and peptides with a hydrophobic C-terminus, while it has weak activity toward peptides with charged C-terminus. May play a role in the inactivation of peptide hormones. May be involved in the regulation of blood pressure through the inactivation of angiotensin II and/or the generation of bradykinin in the kidney.<ref>PMID:15908954</ref> <ref>PMID:16286653</ref> <ref>PMID:21478864</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that optimizes the peptide cargo of major histocompatibility class I (MHC-I) molecules and regulates adaptive immunity. It has unusual substrate selectivity for length and sequence, resulting in poorly understood effects on the cellular immunopeptidome. To understand substrate selection by ERAP1, we solved 2 crystal structures of the enzyme with bound transition-state pseudopeptide analogs at 1.68 A and 1.72 A. Both peptides have their N terminus bound at the active site and extend away along a large internal cavity, interacting with shallow pockets that can influence selectivity. The longer peptide is disordered through the central region of the cavity and has its C terminus bound in an allosteric pocket of domain IV that features a carboxypeptidase-like structural motif. These structures, along with enzymatic and computational analyses, explain how ERAP1 can select peptides based on length while retaining the broad sequence-specificity necessary for its biological function.
		+
		+	Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1.,Giastas P, Mpakali A, Papakyriakou A, Lelis A, Kokkala P, Neu M, Rowland P, Liddle J, Georgiadis D, Stratikos E Proc Natl Acad Sci U S A. 2019 Dec 16. pii: 1912070116. doi:, 10.1073/pnas.1912070116. PMID:31843903<ref>PMID:31843903</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ryf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Giastas, P]]	+	[[Category: Giastas P]]
-	[[Category: Stratikos, E]]	+	[[Category: Stratikos E]]
-	~~[[Category: Antigen presentation]]~~	+
-	~~[[Category: Endoplasmic reticulum aminopeptidase 1]]~~	+
-	~~[[Category: Erap1]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:53, 18 December 2019

OCA — Wed, 18 Dec 2019 07:53:13 GMT

←Older revision		Revision as of 07:53, 18 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ryf is ~~ON HOLD~~	+	==High-resolution crystal structure of ERAP1 in complex with 15mer phosphinic peptide==
-		+	<StructureSection load='6ryf' size='340' side='right'caption='[[6ryf]], [[Resolution\|resolution]] 1.72Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ryf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RYF FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PPI:PROPANOIC+ACID'>PPI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KF2:'>KF2</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6rqx\|6rqx]]</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=6ryf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ryf OCA], [http://pdbe.org/6ryf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ryf RCSB], [http://www.ebi.ac.uk/pdbsum/6ryf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ryf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ERAP1_HUMAN ERAP1_HUMAN]] Aminopeptidase that plays a central role in peptide trimming, a step required for the generation of most HLA class I-binding peptides. Peptide trimming is essential to customize longer precursor peptides to fit them to the correct length required for presentation on MHC class I molecules. Strongly prefers substrates 9-16 residues long. Rapidly degrades 13-mer to a 9-mer and then stops. Preferentially hydrolyzes the residue Leu and peptides with a hydrophobic C-terminus, while it has weak activity toward peptides with charged C-terminus. May play a role in the inactivation of peptide hormones. May be involved in the regulation of blood pressure through the inactivation of angiotensin II and/or the generation of bradykinin in the kidney.<ref>PMID:15908954</ref> <ref>PMID:16286653</ref> <ref>PMID:21478864</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Giastas, P]]
		+	[[Category: Stratikos, E]]
		+	[[Category: Antigen presentation]]
		+	[[Category: Endoplasmic reticulum aminopeptidase 1]]
		+	[[Category: Erap1]]
		+	[[Category: Hydrolase]]

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

OCA — Wed, 19 Jun 2019 04:31:58 GMT

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

←Older revision

Revision as of 04:31, 19 June 2019

OCA: New page: '''Unreleased structure''' The entry 6ryf is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Jun 2019 04:31:57 GMT

New page: '''Unreleased structure''' The entry 6ryf is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ryf is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6ryf - Revision history

OCA at 12:31, 24 January 2024

OCA at 07:53, 18 December 2019

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

OCA: New page: '''Unreleased structure''' The entry 6ryf is ON HOLD Authors: Description: Category: Unreleased Structures