6pvc: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 6pvc is ~~ON HOLD until Paper~~ Publication

==Structure of human MAIT A-F7 TCR in complex with human MR1-DB28==

== Structural highlights ==

<table><tr><td colspan='2'>[[6pvc]] is a 8 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=6PVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PVC FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96Å</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=P1J:3-[[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-6-yl]carbonylamino]propanoic+acid'>P1J</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=6pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pvc OCA], [https://pdbe.org/6pvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pvc RCSB], [https://www.ebi.ac.uk/pdbsum/6pvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pvc ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

The antigen-presenting molecule MR1 presents riboflavin-based metabolites to Mucosal-Associated Invariant T (MAIT) cells. While MR1 egress to the cell surface is ligand-dependent, the ability of small-molecule ligands to impact on MR1 cellular trafficking remains unknown. Arising from an in silico screen of the MR1 ligand-binding pocket, we identify one ligand, 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoic acid, DB28, as well as an analog, methyl 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoate, NV18.1, that down-regulate MR1 from the cell surface and retain MR1 molecules in the endoplasmic reticulum (ER) in an immature form. DB28 and NV18.1 compete with the known MR1 ligands, 5-OP-RU and acetyl-6-FP, for MR1 binding and inhibit MR1-dependent MAIT cell activation. Crystal structures of the MAIT T cell receptor (TCR) complexed with MR1-DB28 and MR1-NV18.1, show that these two ligands reside within the A'-pocket of MR1. Neither ligand forms a Schiff base with MR1 molecules; both are nevertheless sequestered by a network of hydrophobic and polar contacts. Accordingly, we define a class of compounds that inhibits MR1 cellular trafficking.

~~Authors~~:

Ligand-dependent downregulation of MR1 cell surface expression.,Salio M, Awad W, Veerapen N, Gonzalez-Lopez C, Kulicke C, Waithe D, Martens AWJ, Lewinsohn DM, Hobrath JV, Cox LR, Rossjohn J, Besra GS, Cerundolo V Proc Natl Acad Sci U S A. 2020 Apr 27. pii: 2003136117. doi:, 10.1073/pnas.2003136117. PMID:32341160<ref>PMID:32341160</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</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 ==

__TOC__

</StructureSection>

[[Category: Homo sapiens]]

[[Category: Large Structures]]

[[Category: Awad W]]

[[Category: Rossjohn J]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6pvc is ON HOLD  until Paper Publication
+==Structure of human MAIT A-F7 TCR in complex with human MR1-DB28==
+<StructureSection load='6pvc' size='340' side='right'caption='[[6pvc]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6pvc]] is a 8 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=6PVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PVC FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96&#8491;</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=P1J:3-[[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-6-yl]carbonylamino]propanoic+acid'>P1J</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=6pvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pvc OCA], [https://pdbe.org/6pvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pvc RCSB], [https://www.ebi.ac.uk/pdbsum/6pvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pvc ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The antigen-presenting molecule MR1 presents riboflavin-based metabolites to Mucosal-Associated Invariant T (MAIT) cells. While MR1 egress to the cell surface is ligand-dependent, the ability of small-molecule ligands to impact on MR1 cellular trafficking remains unknown. Arising from an in silico screen of the MR1 ligand-binding pocket, we identify one ligand, 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoic acid, DB28, as well as an analog, methyl 3-([2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl]formamido)propanoate, NV18.1, that down-regulate MR1 from the cell surface and retain MR1 molecules in the endoplasmic reticulum (ER) in an immature form. DB28 and NV18.1 compete with the known MR1 ligands, 5-OP-RU and acetyl-6-FP, for MR1 binding and inhibit MR1-dependent MAIT cell activation. Crystal structures of the MAIT T cell receptor (TCR) complexed with MR1-DB28 and MR1-NV18.1, show that these two ligands reside within the A'-pocket of MR1. Neither ligand forms a Schiff base with MR1 molecules; both are nevertheless sequestered by a network of hydrophobic and polar contacts. Accordingly, we define a class of compounds that inhibits MR1 cellular trafficking.
-Authors:
+Ligand-dependent downregulation of MR1 cell surface expression.,Salio M, Awad W, Veerapen N, Gonzalez-Lopez C, Kulicke C, Waithe D, Martens AWJ, Lewinsohn DM, Hobrath JV, Cox LR, Rossjohn J, Besra GS, Cerundolo V Proc Natl Acad Sci U S A. 2020 Apr 27. pii: 2003136117. doi:, 10.1073/pnas.2003136117. PMID:32341160<ref>PMID:32341160</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6pvc" 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/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Awad W]]
+[[Category: Rossjohn J]]